AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0958550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0958550 MtrunA17_Chr6g0485551 59.483 116 39 2 1 116 1 108 1.17e-39 132
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGCTGAAATTCTGGAAATA+AGG 0.320988 6_3:+72524021 Msa0958550:CDS
TCAGGACCCACATATAATTA+TGG 0.337723 6_3:+72523548 Msa0958550:CDS
TTCAATCACTTCATCATAAT+AGG 0.365862 6_3:-72523741 None:intergenic
AATTATGGCAAAAGGAGATC+TGG 0.371566 6_3:+72523563 Msa0958550:CDS
GGAAGCTGAAAGGAAGGAAA+AGG 0.444058 6_3:+72524085 Msa0958550:CDS
AGAGGAGGAAGCTGAAAGGA+AGG 0.454150 6_3:+72524079 Msa0958550:CDS
TCGTGATTTAAATCAGCATC+AGG 0.464071 6_3:-72523788 None:intergenic
AGAAATCTAAGCCAACTACT+TGG 0.472779 6_3:+72523519 Msa0958550:CDS
AGGAGGAAGCTGAAATGAAA+AGG 0.473270 6_3:+72524051 Msa0958550:CDS
GGAAGCTGAAATGAAAAGGA+AGG 0.493440 6_3:+72524055 Msa0958550:CDS
TCTGGAAATAAGGAAGGAAA+AGG 0.493692 6_3:+72524031 Msa0958550:CDS
AGCTGAAAGGAAGGAAAAGG+AGG 0.497172 6_3:+72524088 Msa0958550:CDS
CCAACTACTTGGGTCATCTC+AGG 0.497404 6_3:+72523530 Msa0958550:CDS
CCACATATAATTATGGCAAA+AGG 0.513516 6_3:+72523555 Msa0958550:CDS
AGGAAGAGGAGGAAGCTGAA+AGG 0.516462 6_3:+72524075 Msa0958550:CDS
GAAATCTAAGCCAACTACTT+GGG 0.528517 6_3:+72523520 Msa0958550:CDS
TGAAATGAAAAGGAAGGAAG+AGG 0.532757 6_3:+72524061 Msa0958550:CDS
ATTATGGCAAAAGGAGATCT+GGG 0.533808 6_3:+72523564 Msa0958550:CDS
CCTGAGATGACCCAAGTAGT+TGG 0.545425 6_3:-72523530 None:intergenic
GGAAATAAGGAAGGAAAAGG+AGG 0.550433 6_3:+72524034 Msa0958550:CDS
TGAAATTCTGGAAATAAGGA+AGG 0.567609 6_3:+72524025 Msa0958550:CDS
AATGAAAAGGAAGGAAGAGG+AGG 0.596938 6_3:+72524064 Msa0958550:CDS
TGATGCTGATTTAAATCACG+AGG 0.690474 6_3:+72523790 Msa0958550:CDS
TCTTCCACAAATGACTGACG+AGG 0.715715 6_3:+72523496 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTATAGAAAATAATAATAAA+GGG - chr6_3:72523702-72523721 None:intergenic 10.0%
!!! ATTTTTTAATATAAGTTTGC+CGG - chr6_3:72523597-72523616 None:intergenic 15.0%
!! GGTATAGAAAATAATAATAA+AGG - chr6_3:72523703-72523722 None:intergenic 15.0%
!! TGAAAAAGCAAATTAAAAAA+AGG + chr6_3:72523998-72524017 Msa0958550:intron 15.0%
!! ATAATAATAAAGGGCTAAAA+CGG - chr6_3:72523693-72523712 None:intergenic 20.0%
!! GAAAAAGAAAATGAAAAAGA+AGG + chr6_3:72524160-72524179 Msa0958550:CDS 20.0%
!! CTTTTGCCATAATTATATGT+GGG - chr6_3:72523557-72523576 None:intergenic 25.0%
! TTCAATCACTTCATCATAAT+AGG - chr6_3:72523744-72523763 None:intergenic 25.0%
!! TGAAATTCTGAAAAAAAGCA+AGG + chr6_3:72524115-72524134 Msa0958550:CDS 25.0%
! CCTTTTGCCATAATTATATG+TGG - chr6_3:72523558-72523577 None:intergenic 30.0%
CCACATATAATTATGGCAAA+AGG + chr6_3:72523555-72523574 Msa0958550:CDS 30.0%
!!! AATATAAGTTTGCCGGTTTT+TGG - chr6_3:72523590-72523609 None:intergenic 30.0%
AAAAAATGATACAGATCACC+AGG + chr6_3:72523610-72523629 Msa0958550:CDS 30.0%
AAAAAAGGAAGCTGAAATTC+TGG + chr6_3:72524013-72524032 Msa0958550:intron 30.0%
! AAGCTGAAATTCTGGAAATA+AGG + chr6_3:72524021-72524040 Msa0958550:CDS 30.0%
! TGAAATTCTGGAAATAAGGA+AGG + chr6_3:72524025-72524044 Msa0958550:CDS 30.0%
GAAAAAAAGCAAGGAAAAGA+AGG + chr6_3:72524124-72524143 Msa0958550:CDS 30.0%
CTAAAAAAGTTTGTGAGGAA+GGG + chr6_3:72524207-72524226 Msa0958550:CDS 30.0%
TAAAAAAGTTTGTGAGGAAG+GGG + chr6_3:72524208-72524227 Msa0958550:CDS 30.0%
AGAAATCTAAGCCAACTACT+TGG + chr6_3:72523519-72523538 Msa0958550:CDS 35.0%
GAAATCTAAGCCAACTACTT+GGG + chr6_3:72523520-72523539 Msa0958550:CDS 35.0%
TCAGGACCCACATATAATTA+TGG + chr6_3:72523548-72523567 Msa0958550:CDS 35.0%
AATTATGGCAAAAGGAGATC+TGG + chr6_3:72523563-72523582 Msa0958550:CDS 35.0%
ATTATGGCAAAAGGAGATCT+GGG + chr6_3:72523564-72523583 Msa0958550:CDS 35.0%
AACGATCAAAAAATCATGCC+TGG - chr6_3:72523631-72523650 None:intergenic 35.0%
AGGAATCAAAAAACTTCTGC+AGG - chr6_3:72523724-72523743 None:intergenic 35.0%
TCGTGATTTAAATCAGCATC+AGG - chr6_3:72523791-72523810 None:intergenic 35.0%
!! TGATGCTGATTTAAATCACG+AGG + chr6_3:72523790-72523809 Msa0958550:CDS 35.0%
! TCGAAGTTCTTTACGGTTTT+CGG - chr6_3:72523974-72523993 None:intergenic 35.0%
AAAACCGTAAAGAACTTCGA+AGG + chr6_3:72523974-72523993 Msa0958550:intron 35.0%
TCTGGAAATAAGGAAGGAAA+AGG + chr6_3:72524031-72524050 Msa0958550:CDS 35.0%
TGAAATGAAAAGGAAGGAAG+AGG + chr6_3:72524061-72524080 Msa0958550:CDS 35.0%
AGCAGCTAAAAAAGTTTGTG+AGG + chr6_3:72524202-72524221 Msa0958550:CDS 35.0%
GCTAAAAAAGTTTGTGAGGA+AGG + chr6_3:72524206-72524225 Msa0958550:CDS 35.0%
!! CTAAACAACTGCTGGTTTAG+AGG - chr6_3:72523904-72523923 None:intergenic 40.0%
CTCTAAACCAGCAGTTGTTT+AGG + chr6_3:72523902-72523921 Msa0958550:intron 40.0%
! TTTTCAGCCTAAACAACTGC+TGG - chr6_3:72523912-72523931 None:intergenic 40.0%
TCAGCCTTCGAAGTTCTTTA+CGG - chr6_3:72523981-72524000 None:intergenic 40.0%
GGAAATAAGGAAGGAAAAGG+AGG + chr6_3:72524034-72524053 Msa0958550:CDS 40.0%
AGGAGGAAGCTGAAATGAAA+AGG + chr6_3:72524051-72524070 Msa0958550:CDS 40.0%
GGAAGCTGAAATGAAAAGGA+AGG + chr6_3:72524055-72524074 Msa0958550:CDS 40.0%
AATGAAAAGGAAGGAAGAGG+AGG + chr6_3:72524064-72524083 Msa0958550:CDS 40.0%
TGTTTAGGCTGAAAACTGCG+TGG + chr6_3:72523917-72523936 Msa0958550:intron 45.0%
! AAAACTGCGTGGTTTGGCAA+AGG + chr6_3:72523928-72523947 Msa0958550:intron 45.0%
GGAAGCTGAAAGGAAGGAAA+AGG + chr6_3:72524085-72524104 Msa0958550:CDS 45.0%
AGCTGAAAGGAAGGAAAAGG+AGG + chr6_3:72524088-72524107 Msa0958550:CDS 45.0%
CCTGAGATGACCCAAGTAGT+TGG - chr6_3:72523533-72523552 None:intergenic 50.0%
CCAACTACTTGGGTCATCTC+AGG + chr6_3:72523530-72523549 Msa0958550:CDS 50.0%
AGGAGATCTGGGCCAAAAAC+CGG + chr6_3:72523575-72523594 Msa0958550:CDS 50.0%
AGGCTGAAAACTGCGTGGTT+TGG + chr6_3:72523922-72523941 Msa0958550:intron 50.0%
AGGAAGAGGAGGAAGCTGAA+AGG + chr6_3:72524075-72524094 Msa0958550:CDS 50.0%
AGAGGAGGAAGCTGAAAGGA+AGG + chr6_3:72524079-72524098 Msa0958550:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 72523506 72524244 72523506 ID=Msa0958550;Name=Msa0958550
chr6_3 mRNA 72523506 72524244 72523506 ID=Msa0958550-mRNA-1;Parent=Msa0958550;Name=Msa0958550-mRNA-1;_AED=0.33;_eAED=0.34;_QI=0|0|0|1|1|1|3|0|144
chr6_3 exon 72523506 72523631 72523506 ID=Msa0958550-mRNA-1:exon:13220;Parent=Msa0958550-mRNA-1
chr6_3 exon 72523728 72523811 72523728 ID=Msa0958550-mRNA-1:exon:13221;Parent=Msa0958550-mRNA-1
chr6_3 exon 72524020 72524244 72524020 ID=Msa0958550-mRNA-1:exon:13222;Parent=Msa0958550-mRNA-1
chr6_3 CDS 72523506 72523631 72523506 ID=Msa0958550-mRNA-1:cds;Parent=Msa0958550-mRNA-1
chr6_3 CDS 72523728 72523811 72523728 ID=Msa0958550-mRNA-1:cds;Parent=Msa0958550-mRNA-1
chr6_3 CDS 72524020 72524244 72524020 ID=Msa0958550-mRNA-1:cds;Parent=Msa0958550-mRNA-1
Gene Sequence

>Msa0958550

ATGACTGACGAGGAGAAATCTAAGCCAACTACTTGGGTCATCTCAGGACCCACATATAATTATGGCAAAAGGAGATCTGGGCCAAAAACCGGCAAACTTATATTAAAAAATGATACAGATCACCAGAAGTTTTTTGATTCCTATTATGATGAAGTGATTGAAGATGTTCGTAGTTGCATGAATAAGCCTGATGCTGATTTAAATCACGAGGAAGCTGAAATTCTGGAAATAAGGAAGGAAAAGGAGGAAGCTGAAATGAAAAGGAAGGAAGAGGAGGAAGCTGAAAGGAAGGAAAAGGAGGAAGCTGAAATTCTGAAAAAAAGCAAGGAAAAGAAGGAAGCTAAAATTCAGAAAAAGAAAATGAAAAAGAAGGAAGCTAAAATTCGAAAGCAAGCAGCTAAAAAAGTTTGTGAGGAAGGGGCTAAAGCATGTTAA

Protein sequence

>Msa0958550

MTDEEKSKPTTWVISGPTYNYGKRRSGPKTGKLILKNDTDHQKFFDSYYDEVIEDVRSCMNKPDADLNHEEAEILEIRKEKEEAEMKRKEEEEAERKEKEEAEILKKSKEKKEAKIQKKKMKKKEAKIRKQAAKKVCEEGAKAC*