AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0688960


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0688960 MtrunA17_Chr4g0018731 78.846 104 16 2 27 126 71 172 5.57e-27 99.4
Msa0688960 MtrunA17_Chr1g0168301 81.897 116 17 1 27 138 210 325 3.21e-19 81.6
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 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGGAGTGTTTAAGACTAAC+AGG 0.286414 4_4:-55420893 Msa0688960:CDS
ATCATCAACTGACAGTGATT+CGG 0.382705 4_4:-55420655 Msa0688960:CDS
AAAGGAGGAGGAGGGAGCAC+AGG 0.386258 4_4:-55420842 Msa0688960:CDS
TCATCAACTGACAGTGATTC+GGG 0.386672 4_4:-55420654 Msa0688960:CDS
GATTCGGGTGATGGATATAA+TGG 0.404972 4_4:-55420639 Msa0688960:CDS
ACCATGGAGATGATGATTAG+AGG 0.412561 4_4:-55420566 None:intergenic
TGGATATAATGGTTCAAGTA+AGG 0.433386 4_4:-55420628 Msa0688960:CDS
CTATATTCATCACTATCATC+TGG 0.440092 4_4:+55420798 None:intergenic
GCTAGTGATTCAGATGGTTC+CGG 0.468678 4_4:-55420867 Msa0688960:CDS
ACTGACAGTGATTCGGGTGA+TGG 0.486358 4_4:-55420648 Msa0688960:CDS
CTCCCTCCTCCTCCTTTCAC+CGG 0.487250 4_4:+55420848 None:intergenic
GTAGGAAAGAGAAGAGGAGA+AGG 0.494224 4_4:-55420758 Msa0688960:CDS
ACAAAGATGCTGACCGAAAG+AGG 0.498522 4_4:-55420939 Msa0688960:CDS
ATTCAGATGGTTCCGGTGAA+AGG 0.502557 4_4:-55420860 Msa0688960:CDS
TCCTCTAATCATCATCTCCA+TGG 0.523954 4_4:+55420565 None:intergenic
GTTCCGGTGAAAGGAGGAGG+AGG 0.525308 4_4:-55420851 Msa0688960:CDS
ATGAATATAGACACAAGAAA+AGG 0.532593 4_4:-55420785 Msa0688960:CDS
GGATATAATGGTTCAAGTAA+GGG 0.549938 4_4:-55420627 Msa0688960:CDS
ATGGTTCCGGTGAAAGGAGG+AGG 0.558346 4_4:-55420854 Msa0688960:CDS
TAATGGTTCAAGTAAGGGTA+GGG 0.560844 4_4:-55420622 Msa0688960:CDS
GACACAAGAAAAGGAAGAGT+AGG 0.567421 4_4:-55420776 Msa0688960:CDS
TTCTGATTCTGAAACATCTG+AGG 0.573778 4_4:-55420718 Msa0688960:CDS
AGAGAGGTAGAGAAAAGAGA+AGG 0.579127 4_4:-55420912 Msa0688960:CDS
ATAATGGTTCAAGTAAGGGT+AGG 0.582111 4_4:-55420623 Msa0688960:CDS
GGAAGAGTAGGAAAGAGAAG+AGG 0.590104 4_4:-55420764 Msa0688960:CDS
GGGAGCACAGGAGAAGCATG+AGG 0.590249 4_4:-55420830 Msa0688960:CDS
AAGAGGAGGAGACGCCACCA+TGG 0.594257 4_4:-55420582 Msa0688960:CDS
CAGATGGTTCCGGTGAAAGG+AGG 0.617536 4_4:-55420857 Msa0688960:CDS
CATCTGAGGATTCTACTTCG+CGG 0.617958 4_4:-55420704 Msa0688960:CDS
AGGGAAGCTAGTGATTCAGA+TGG 0.649064 4_4:-55420873 Msa0688960:CDS
GGAGCACAGGAGAAGCATGA+GGG 0.656858 4_4:-55420829 Msa0688960:CDS
TTCCGGTGAAAGGAGGAGGA+GGG 0.666380 4_4:-55420850 Msa0688960:CDS
AGGAGTGTTTAAGACTAACA+GGG 0.683554 4_4:-55420892 Msa0688960:CDS
TCTAATCATCATCTCCATGG+TGG 0.691101 4_4:+55420568 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATCAAAAAATCAGAAAAG+AGG - chr4_4:55420933-55420952 Msa0688960:CDS 20.0%
! ATGAATATAGACACAAGAAA+AGG - chr4_4:55420747-55420766 Msa0688960:CDS 25.0%
CTATATTCATCACTATCATC+TGG + chr4_4:55420737-55420756 None:intergenic 30.0%
TGGATATAATGGTTCAAGTA+AGG - chr4_4:55420904-55420923 Msa0688960:CDS 30.0%
GGATATAATGGTTCAAGTAA+GGG - chr4_4:55420905-55420924 Msa0688960:CDS 30.0%
TCAAAAAATCAGAAAAGAGG+AGG - chr4_4:55420936-55420955 Msa0688960:CDS 30.0%
! TACCTCTCTTTTTCCTCTTT+CGG + chr4_4:55420609-55420628 None:intergenic 35.0%
!! AAGGAGTGTTTAAGACTAAC+AGG - chr4_4:55420639-55420658 Msa0688960:CDS 35.0%
!! AGGAGTGTTTAAGACTAACA+GGG - chr4_4:55420640-55420659 Msa0688960:CDS 35.0%
!! TTCTGATTCTGAAACATCTG+AGG - chr4_4:55420814-55420833 Msa0688960:CDS 35.0%
ATCATCAACTGACAGTGATT+CGG - chr4_4:55420877-55420896 Msa0688960:CDS 35.0%
ATAATGGTTCAAGTAAGGGT+AGG - chr4_4:55420909-55420928 Msa0688960:CDS 35.0%
TAATGGTTCAAGTAAGGGTA+GGG - chr4_4:55420910-55420929 Msa0688960:CDS 35.0%
AGAGAGGTAGAGAAAAGAGA+AGG - chr4_4:55420620-55420639 Msa0688960:CDS 40.0%
GACACAAGAAAAGGAAGAGT+AGG - chr4_4:55420756-55420775 Msa0688960:CDS 40.0%
TCATCAACTGACAGTGATTC+GGG - chr4_4:55420878-55420897 Msa0688960:CDS 40.0%
!! GATTCGGGTGATGGATATAA+TGG - chr4_4:55420893-55420912 Msa0688960:CDS 40.0%
ACAAAGATGCTGACCGAAAG+AGG - chr4_4:55420593-55420612 Msa0688960:CDS 45.0%
GACCGAAAGAGGAAAAAGAG+AGG - chr4_4:55420604-55420623 Msa0688960:CDS 45.0%
AGGGAAGCTAGTGATTCAGA+TGG - chr4_4:55420659-55420678 Msa0688960:CDS 45.0%
GCTAGTGATTCAGATGGTTC+CGG - chr4_4:55420665-55420684 Msa0688960:CDS 45.0%
ATTCAGATGGTTCCGGTGAA+AGG - chr4_4:55420672-55420691 Msa0688960:CDS 45.0%
GGAAGAGTAGGAAAGAGAAG+AGG - chr4_4:55420768-55420787 Msa0688960:CDS 45.0%
GTAGGAAAGAGAAGAGGAGA+AGG - chr4_4:55420774-55420793 Msa0688960:CDS 45.0%
CATCTGAGGATTCTACTTCG+CGG - chr4_4:55420828-55420847 Msa0688960:CDS 45.0%
! ACTGACAGTGATTCGGGTGA+TGG - chr4_4:55420884-55420903 Msa0688960:CDS 50.0%
CAGATGGTTCCGGTGAAAGG+AGG - chr4_4:55420675-55420694 Msa0688960:CDS 55.0%
ATGGTTCCGGTGAAAGGAGG+AGG - chr4_4:55420678-55420697 Msa0688960:CDS 55.0%
TTCCGGTGAAAGGAGGAGGA+GGG - chr4_4:55420682-55420701 Msa0688960:CDS 55.0%
! GGAGCACAGGAGAAGCATGA+GGG - chr4_4:55420703-55420722 Msa0688960:CDS 55.0%
GTTCCGGTGAAAGGAGGAGG+AGG - chr4_4:55420681-55420700 Msa0688960:CDS 60.0%
CTCCCTCCTCCTCCTTTCAC+CGG + chr4_4:55420687-55420706 None:intergenic 60.0%
! AAAGGAGGAGGAGGGAGCAC+AGG - chr4_4:55420690-55420709 Msa0688960:CDS 60.0%
! GGGAGCACAGGAGAAGCATG+AGG - chr4_4:55420702-55420721 Msa0688960:CDS 60.0%
AAGAGGAGGAGACGCCACCA+TGG - chr4_4:55420950-55420969 Msa0688960:CDS 60.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 55420569 55420985 55420569 ID=Msa0688960;Name=Msa0688960
chr4_4 mRNA 55420569 55420985 55420569 ID=Msa0688960-mRNA-1;Parent=Msa0688960;Name=Msa0688960-mRNA-1;_AED=0.39;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|138
chr4_4 exon 55420569 55420985 55420569 ID=Msa0688960-mRNA-1:exon:14621;Parent=Msa0688960-mRNA-1
chr4_4 CDS 55420569 55420985 55420569 ID=Msa0688960-mRNA-1:cds;Parent=Msa0688960-mRNA-1
Gene Sequence

>Msa0688960

ATGACTAAGATGATGACGAGTCAGACAAAGATGCTGACCGAAAGAGGAAAAAGAGAGGTAGAGAAAAGAGAAGGAGTGTTTAAGACTAACAGGGAAGCTAGTGATTCAGATGGTTCCGGTGAAAGGAGGAGGAGGGAGCACAGGAGAAGCATGAGGGACGAGTCTCCAGATGATAGTGATGAATATAGACACAAGAAAAGGAAGAGTAGGAAAGAGAAGAGGAGAAGGAGAAGTCGTCTTTCAGATTCTGATTCTGAAACATCTGAGGATTCTACTTCGCGGCACAAGCGAAATAGCAAGAGAACTTCATCATCAACTGACAGTGATTCGGGTGATGGATATAATGGTTCAAGTAAGGGTAGGGATATCAAAAAATCAGAAAAGAGGAGGAGACGCCACCATGGAGATGATGATTAG

Protein sequence

>Msa0688960

MTKMMTSQTKMLTERGKREVEKREGVFKTNREASDSDGSGERRRREHRRSMRDESPDDSDEYRHKKRKSRKEKRRRRSRLSDSDSETSEDSTSRHKRNSKRTSSSTDSDSGDGYNGSSKGRDIKKSEKRRRRHHGDDD*