AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0899450


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0899450 MtrunA17_Chr6g0485551 78.283 198 23 3 1 180 1 196 3.05e-62 191
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 34 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGGACCCACATATAATTA+TGG 0.337723 6_1:-94575235 Msa0899450:CDS
TCAGCCTTCGAAGTTCTTTA+CGG 0.344809 6_1:+94574802 None:intergenic
AAGTTGAAATTCTGGAAATA+AGG 0.355807 6_1:-94574758 Msa0899450:CDS
TTCAATCACTTCATCATAAT+AGG 0.366272 6_1:+94575040 None:intergenic
AATTATGGCAAAAGGAGATC+TGG 0.371566 6_1:-94575220 Msa0899450:CDS
ATTATTGATGAGAAGTTTGC+CGG 0.385556 6_1:+94575189 None:intergenic
AGGCTGAAAACTGCGTGGTT+TGG 0.421494 6_1:-94574858 Msa0899450:CDS
GGAAGCTGAAAGGAAGGAAA+AGG 0.444058 6_1:-94574694 Msa0899450:CDS
AGAGGAGGAAGCTGAAAGGA+AGG 0.454150 6_1:-94574700 Msa0899450:CDS
CTCTAAACCAGCAGTTGTTT+AGG 0.457152 6_1:-94574878 Msa0899450:intron
TCGTGATTTAAATCAGCATC+AGG 0.464071 6_1:+94574993 None:intergenic
GAAAATAAGCAAGGAAAAGA+AGG 0.471895 6_1:-94574655 Msa0899450:CDS
AGAAATCTAAGCCAACTACT+TGG 0.472779 6_1:-94575264 Msa0899450:CDS
AGGAGGAAGCTGAAATGAAA+AGG 0.473270 6_1:-94574728 Msa0899450:CDS
GGAAGCTGAAATGAAAAGGA+AGG 0.493440 6_1:-94574724 Msa0899450:CDS
TCTGGAAATAAGGAAGGAAA+AGG 0.493692 6_1:-94574748 Msa0899450:CDS
AGCTGAAAGGAAGGAAAAGG+AGG 0.497172 6_1:-94574691 Msa0899450:CDS
CCAACTACTTGGGTCATCTC+AGG 0.497404 6_1:-94575253 Msa0899450:CDS
CCACATATAATTATGGCAAA+AGG 0.513516 6_1:-94575228 Msa0899450:CDS
AGGAAGAGGAGGAAGCTGAA+AGG 0.516462 6_1:-94574704 Msa0899450:CDS
GAAATCTAAGCCAACTACTT+GGG 0.528517 6_1:-94575263 Msa0899450:CDS
CAATAATGATAGAGATCACC+AGG 0.531064 6_1:-94575173 Msa0899450:intron
TGAAATTCTGGAAATAAGGA+AGG 0.531101 6_1:-94574754 Msa0899450:CDS
TGAAATGAAAAGGAAGGAAG+AGG 0.532757 6_1:-94574718 Msa0899450:CDS
ATTATGGCAAAAGGAGATCT+GGG 0.533808 6_1:-94575219 Msa0899450:CDS
CCTGAGATGACCCAAGTAGT+TGG 0.545425 6_1:+94575253 None:intergenic
GGAAATAAGGAAGGAAAAGG+AGG 0.550433 6_1:-94574745 Msa0899450:CDS
AAAACTGCGTGGTTTGGCAA+AGG 0.574300 6_1:-94574852 Msa0899450:CDS
AATGAAAAGGAAGGAAGAGG+AGG 0.596938 6_1:-94574715 Msa0899450:CDS
TGAAATTCTGAAAATAAGCA+AGG 0.597576 6_1:-94574664 Msa0899450:CDS
AAAACCGTAAAGAACTTCGA+AGG 0.658384 6_1:-94574806 Msa0899450:CDS
TGATGCTGATTTAAATCACG+AGG 0.690474 6_1:-94574991 Msa0899450:intron
TGTTTAGGCTGAAAACTGCG+TGG 0.725223 6_1:-94574863 Msa0899450:CDS
TCTTCCACAAATGACTGACG+AGG 0.728254 6_1:-94575287 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTATAGAAAATTAATATTAA+AGG + chr6_1:94574755-94574774 None:intergenic 10.0%
!! GAAAAAGCAAATTAAAAAAA+AGG - chr6_1:94575053-94575072 Msa0899450:CDS 15.0%
!! TTAATATTAAAGGGCTAAAA+CGG + chr6_1:94574745-94574764 None:intergenic 20.0%
!! GAAAAAGAAAATGAAAAAGA+AGG - chr6_1:94575215-94575234 Msa0899450:CDS 20.0%
!! CTTTTGCCATAATTATATGT+GGG + chr6_1:94574608-94574627 None:intergenic 25.0%
! TTCAATCACTTCATCATAAT+AGG + chr6_1:94574797-94574816 None:intergenic 25.0%
! AAAAAAGGAAGTTGAAATTC+TGG - chr6_1:94575068-94575087 Msa0899450:intron 25.0%
!! AAGTTGAAATTCTGGAAATA+AGG - chr6_1:94575076-94575095 Msa0899450:intron 25.0%
!! TGAAATTCTGAAAATAAGCA+AGG - chr6_1:94575170-94575189 Msa0899450:intron 25.0%
! CCTTTTGCCATAATTATATG+TGG + chr6_1:94574609-94574628 None:intergenic 30.0%
CCACATATAATTATGGCAAA+AGG - chr6_1:94574606-94574625 Msa0899450:CDS 30.0%
ATTATTGATGAGAAGTTTGC+CGG + chr6_1:94574648-94574667 None:intergenic 30.0%
! TGAAATTCTGGAAATAAGGA+AGG - chr6_1:94575080-94575099 Msa0899450:intron 30.0%
GAAAATAAGCAAGGAAAAGA+AGG - chr6_1:94575179-94575198 Msa0899450:CDS 30.0%
CTAAAAAAGTTTGTGAGGAA+GGG - chr6_1:94575262-94575281 Msa0899450:CDS 30.0%
TAAAAAAGTTTGTGAGGAAG+GGG - chr6_1:94575263-94575282 Msa0899450:CDS 30.0%
AGAAATCTAAGCCAACTACT+TGG - chr6_1:94574570-94574589 Msa0899450:CDS 35.0%
GAAATCTAAGCCAACTACTT+GGG - chr6_1:94574571-94574590 Msa0899450:CDS 35.0%
TCAGGACCCACATATAATTA+TGG - chr6_1:94574599-94574618 Msa0899450:CDS 35.0%
AATTATGGCAAAAGGAGATC+TGG - chr6_1:94574614-94574633 Msa0899450:CDS 35.0%
ATTATGGCAAAAGGAGATCT+GGG - chr6_1:94574615-94574634 Msa0899450:CDS 35.0%
CAATAATGATAGAGATCACC+AGG - chr6_1:94574661-94574680 Msa0899450:CDS 35.0%
ACGATCAAAAAAATCATGCC+TGG + chr6_1:94574682-94574701 None:intergenic 35.0%
AGGAATCAAAAAACTTCTGC+AGG + chr6_1:94574777-94574796 None:intergenic 35.0%
TCGTGATTTAAATCAGCATC+AGG + chr6_1:94574844-94574863 None:intergenic 35.0%
!! TGATGCTGATTTAAATCACG+AGG - chr6_1:94574843-94574862 Msa0899450:CDS 35.0%
! TCGAAGTTCTTTACGGTTTT+CGG + chr6_1:94575028-94575047 None:intergenic 35.0%
AAAACCGTAAAGAACTTCGA+AGG - chr6_1:94575028-94575047 Msa0899450:CDS 35.0%
TCTGGAAATAAGGAAGGAAA+AGG - chr6_1:94575086-94575105 Msa0899450:intron 35.0%
TGAAATGAAAAGGAAGGAAG+AGG - chr6_1:94575116-94575135 Msa0899450:intron 35.0%
AGCAGCTAAAAAAGTTTGTG+AGG - chr6_1:94575257-94575276 Msa0899450:CDS 35.0%
GCTAAAAAAGTTTGTGAGGA+AGG - chr6_1:94575261-94575280 Msa0899450:CDS 35.0%
!!! ATGAGAAGTTTGCCGGTTTT+TGG + chr6_1:94574641-94574660 None:intergenic 40.0%
!! CTAAACAACTGCTGGTTTAG+AGG + chr6_1:94574958-94574977 None:intergenic 40.0%
CTCTAAACCAGCAGTTGTTT+AGG - chr6_1:94574956-94574975 Msa0899450:intron 40.0%
! TTTTCAGCCTAAACAACTGC+TGG + chr6_1:94574966-94574985 None:intergenic 40.0%
TCAGCCTTCGAAGTTCTTTA+CGG + chr6_1:94575035-94575054 None:intergenic 40.0%
GGAAATAAGGAAGGAAAAGG+AGG - chr6_1:94575089-94575108 Msa0899450:intron 40.0%
AGGAGGAAGCTGAAATGAAA+AGG - chr6_1:94575106-94575125 Msa0899450:intron 40.0%
GGAAGCTGAAATGAAAAGGA+AGG - chr6_1:94575110-94575129 Msa0899450:intron 40.0%
AATGAAAAGGAAGGAAGAGG+AGG - chr6_1:94575119-94575138 Msa0899450:intron 40.0%
TGTTTAGGCTGAAAACTGCG+TGG - chr6_1:94574971-94574990 Msa0899450:intron 45.0%
! AAAACTGCGTGGTTTGGCAA+AGG - chr6_1:94574982-94575001 Msa0899450:intron 45.0%
GGAAGCTGAAAGGAAGGAAA+AGG - chr6_1:94575140-94575159 Msa0899450:intron 45.0%
AGCTGAAAGGAAGGAAAAGG+AGG - chr6_1:94575143-94575162 Msa0899450:intron 45.0%
!! TATAGAAAATTAATATTAAA+GGG + chr6_1:94574754-94574773 None:intergenic 5.0%
CCTGAGATGACCCAAGTAGT+TGG + chr6_1:94574584-94574603 None:intergenic 50.0%
CCAACTACTTGGGTCATCTC+AGG - chr6_1:94574581-94574600 Msa0899450:CDS 50.0%
AGGAGATCTGGGCCAAAAAC+CGG - chr6_1:94574626-94574645 Msa0899450:CDS 50.0%
AGGCTGAAAACTGCGTGGTT+TGG - chr6_1:94574976-94574995 Msa0899450:intron 50.0%
AGGAAGAGGAGGAAGCTGAA+AGG - chr6_1:94575130-94575149 Msa0899450:intron 50.0%
AGAGGAGGAAGCTGAAAGGA+AGG - chr6_1:94575134-94575153 Msa0899450:intron 50.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 94574557 94575299 94574557 ID=Msa0899450;Name=Msa0899450
chr6_1 mRNA 94574557 94575299 94574557 ID=Msa0899450-mRNA-1;Parent=Msa0899450;Name=Msa0899450-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0|0|1|1|1|3|0|180
chr6_1 exon 94575174 94575299 94575174 ID=Msa0899450-mRNA-1:exon:16150;Parent=Msa0899450-mRNA-1
chr6_1 exon 94574992 94575075 94574992 ID=Msa0899450-mRNA-1:exon:16149;Parent=Msa0899450-mRNA-1
chr6_1 exon 94574557 94574889 94574557 ID=Msa0899450-mRNA-1:exon:16148;Parent=Msa0899450-mRNA-1
chr6_1 CDS 94575174 94575299 94575174 ID=Msa0899450-mRNA-1:cds;Parent=Msa0899450-mRNA-1
chr6_1 CDS 94574992 94575075 94574992 ID=Msa0899450-mRNA-1:cds;Parent=Msa0899450-mRNA-1
chr6_1 CDS 94574557 94574889 94574557 ID=Msa0899450-mRNA-1:cds;Parent=Msa0899450-mRNA-1
Gene Sequence

>Msa0899450

ATGACTGACGAGGAGAAATCTAAGCCAACTACTTGGGTCATCTCAGGACCCACATATAATTATGGCAAAAGGAGATCTGGGCCAAAAACCGGCAAACTTCTCATCAATAATGATAGAGATCACCAGAAGTTTTTTGATTCCTATTATGATGAAGTGATTGAAGACGTTCGTAGTTGCATCAATAAGCCTGATGCTGATTTAAATCACGAGCAGTTGTTTAGGCTGAAAACTGCGTGGTTTGGCAAAGGTCATTATAGAGATTATGTTGCCGAAAACCGTAAAGAACTTCGAAGGCTGAAAAAGCAAATTAAAAAAAAGGAAGTTGAAATTCTGGAAATAAGGAAGGAAAAGGAGGAAGCTGAAATGAAAAGGAAGGAAGAGGAGGAAGCTGAAAGGAAGGAAAAGGAGGAAGCTGAAATTCTGAAAATAAGCAAGGAAAAGAAGGAAGCTAAAATTCAGAAAAAGAAAATGAAAAAGAAGGAAGCTAAAATTCGAAAGCAAGCAGCTAAAAAAGTTTGTGAGGAAGGGGCTAAAGCATGTTAA

Protein sequence

>Msa0899450

MTDEEKSKPTTWVISGPTYNYGKRRSGPKTGKLLINNDRDHQKFFDSYYDEVIEDVRSCINKPDADLNHEQLFRLKTAWFGKGHYRDYVAENRKELRRLKKQIKKKEVEILEIRKEKEEAEMKRKEEEEAERKEKEEAEILKISKEKKEAKIQKKKMKKKEAKIRKQAAKKVCEEGAKAC*