AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0689780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0689780 MtrunA17_Chr5g0404011 91.919 99 5 1 1 99 1 96 7.44e-61 180
Msa0689780 MtrunA17_Chr5g0403991 71.569 102 26 1 1 99 1 102 3.41e-49 151
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAACACAAGAAGAATAAA+AGG 0.259149 4_4:+56996564 Msa0689780:CDS
ATATTCTTCATTTGTCTCCA+TGG 0.393537 4_4:-56996543 None:intergenic
CTCCTCCGCCTCGTTGGGAC+TGG 0.394195 4_4:-56996630 None:intergenic
AAGAAGAATAAAAGGGGTAT+TGG 0.401583 4_4:+56996572 Msa0689780:CDS
CGTCACCTCCTCCGCCTCGT+TGG 0.403234 4_4:-56996636 None:intergenic
GTCACCTCCTCCGCCTCGTT+GGG 0.405210 4_4:-56996635 None:intergenic
ATCAGTCACCACCCTTGAAC+TGG 0.436123 4_4:-56996713 None:intergenic
TCGGAATGTGTTAAAGTTGG+TGG 0.447025 4_4:+56996500 Msa0689780:CDS
CAGTCCCAACGAGGCGGAGG+AGG 0.463123 4_4:+56996631 Msa0689780:CDS
GGAGGAGGTGACGGTGAAGA+AGG 0.476982 4_4:+56996646 Msa0689780:CDS
TGAACACAAGAAGAATAAAA+GGG 0.482825 4_4:+56996565 Msa0689780:CDS
ATCATCAGAATCTGTAACTT+CGG 0.488685 4_4:+56996481 Msa0689780:CDS
TTCCAGTCCCAACGAGGCGG+AGG 0.517997 4_4:+56996628 Msa0689780:CDS
AGGAGAAGAAACGTTCGTCT+TGG 0.533201 4_4:+56996666 Msa0689780:CDS
CAACGAGGCGGAGGAGGTGA+CGG 0.560055 4_4:+56996637 Msa0689780:CDS
ACTTCGGAATGTGTTAAAGT+TGG 0.563777 4_4:+56996497 Msa0689780:CDS
GTTAGGTTGTCAAGATCAGA+AGG 0.595454 4_4:+56996449 Msa0689780:CDS
TGAAAGACTCTCACAAACCA+TGG 0.604467 4_4:+56996526 Msa0689780:CDS
AACGTTGGCCAGTTCAAGGG+TGG 0.624083 4_4:+56996705 Msa0689780:CDS
GAACACAAGAAGAATAAAAG+GGG 0.652443 4_4:+56996566 Msa0689780:CDS
GAGAATTTCCAGTCCCAACG+AGG 0.655349 4_4:+56996622 Msa0689780:CDS
AATTTCCAGTCCCAACGAGG+CGG 0.689181 4_4:+56996625 Msa0689780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGGAATTTAGAAAAAGTGTT+AGG + chr4_4:56996432-56996451 Msa0689780:CDS 25.0%
! ATGAACACAAGAAGAATAAA+AGG + chr4_4:56996564-56996583 Msa0689780:CDS 25.0%
! TGAACACAAGAAGAATAAAA+GGG + chr4_4:56996565-56996584 Msa0689780:CDS 25.0%
ATCATCAGAATCTGTAACTT+CGG + chr4_4:56996481-56996500 Msa0689780:CDS 30.0%
ATATTCTTCATTTGTCTCCA+TGG - chr4_4:56996546-56996565 None:intergenic 30.0%
GAACACAAGAAGAATAAAAG+GGG + chr4_4:56996566-56996585 Msa0689780:CDS 30.0%
! AAGAAGAATAAAAGGGGTAT+TGG + chr4_4:56996572-56996591 Msa0689780:CDS 30.0%
ACTTCGGAATGTGTTAAAGT+TGG + chr4_4:56996497-56996516 Msa0689780:CDS 35.0%
! GTTAGGTTGTCAAGATCAGA+AGG + chr4_4:56996449-56996468 Msa0689780:CDS 40.0%
TCGGAATGTGTTAAAGTTGG+TGG + chr4_4:56996500-56996519 Msa0689780:CDS 40.0%
TGAAAGACTCTCACAAACCA+TGG + chr4_4:56996526-56996545 Msa0689780:CDS 40.0%
TTCCAGATCCACAAAAACGT+TGG + chr4_4:56996690-56996709 Msa0689780:CDS 40.0%
AAAAACGTTGGCCAGTTCAA+GGG + chr4_4:56996702-56996721 Msa0689780:CDS 40.0%
AGGAGAAGAAACGTTCGTCT+TGG + chr4_4:56996666-56996685 Msa0689780:CDS 45.0%
! TGAACTGGCCAACGTTTTTG+TGG - chr4_4:56996701-56996720 None:intergenic 45.0%
CAAAAACGTTGGCCAGTTCA+AGG + chr4_4:56996701-56996720 Msa0689780:CDS 45.0%
GAGAATTTCCAGTCCCAACG+AGG + chr4_4:56996622-56996641 Msa0689780:CDS 50.0%
AATTTCCAGTCCCAACGAGG+CGG + chr4_4:56996625-56996644 Msa0689780:CDS 50.0%
! GGCCAACGTTTTTGTGGATC+TGG - chr4_4:56996695-56996714 None:intergenic 50.0%
AACGTTGGCCAGTTCAAGGG+TGG + chr4_4:56996705-56996724 Msa0689780:CDS 55.0%
! GGAGGAGGTGACGGTGAAGA+AGG + chr4_4:56996646-56996665 Msa0689780:CDS 60.0%
TTCCAGTCCCAACGAGGCGG+AGG + chr4_4:56996628-56996647 Msa0689780:CDS 65.0%
GTCACCTCCTCCGCCTCGTT+GGG - chr4_4:56996638-56996657 None:intergenic 65.0%
CAACGAGGCGGAGGAGGTGA+CGG + chr4_4:56996637-56996656 Msa0689780:CDS 65.0%
CTCCTCCGCCTCGTTGGGAC+TGG - chr4_4:56996633-56996652 None:intergenic 70.0%
CAGTCCCAACGAGGCGGAGG+AGG + chr4_4:56996631-56996650 Msa0689780:CDS 70.0%
CGTCACCTCCTCCGCCTCGT+TGG - chr4_4:56996639-56996658 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 56996431 56996730 56996431 ID=Msa0689780;Name=Msa0689780
chr4_4 mRNA 56996431 56996730 56996431 ID=Msa0689780-mRNA-1;Parent=Msa0689780;Name=Msa0689780-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|99
chr4_4 exon 56996431 56996730 56996431 ID=Msa0689780-mRNA-1:exon:15198;Parent=Msa0689780-mRNA-1
chr4_4 CDS 56996431 56996730 56996431 ID=Msa0689780-mRNA-1:cds;Parent=Msa0689780-mRNA-1
Gene Sequence

>Msa0689780

ATGGAATTTAGAAAAAGTGTTAGGTTGTCAAGATCAGAAGGTATATTACTATCATCAGAATCTGTAACTTCGGAATGTGTTAAAGTTGGTGGTTATGAAAGACTCTCACAAACCATGGAGACAAATGAAGAATATGAACACAAGAAGAATAAAAGGGGTATTGGATTTCTAAGTAAAGTATTAAATTTAACGAGAATTTCCAGTCCCAACGAGGCGGAGGAGGTGACGGTGAAGAAGGAGAAGAAACGTTCGTCTTGGCTTCCAGATCCACAAAAACGTTGGCCAGTTCAAGGGTGGTGA

Protein sequence

>Msa0689780

MEFRKSVRLSRSEGILLSSESVTSECVKVGGYERLSQTMETNEEYEHKKNKRGIGFLSKVLNLTRISSPNEAEEVTVKKEKKRSSWLPDPQKRWPVQGW*