AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0909120


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0909120 MtrunA17_Chr8g0355661 93.750 64 4 0 1 64 1 64 2.23e-39 127
Msa0909120 MtrunA17_Chr8g0355811 87.500 64 8 0 1 64 1 64 8.96e-38 122
Msa0909120 MtrunA17_Chr8g0355741 85.938 64 9 0 1 64 1 64 8.58e-36 117
Msa0909120 MtrunA17_Chr8g0355721 81.250 64 12 0 1 64 1 64 8.91e-36 117
Msa0909120 MtrunA17_Chr8g0355801 82.812 64 11 0 1 64 1 64 1.11e-34 115
Msa0909120 MtrunA17_Chr8g0355821 79.688 64 13 0 1 64 1 64 2.48e-34 114
Msa0909120 MtrunA17_Chr8g0355791 82.812 64 11 0 1 64 1 64 6.09e-34 113
Msa0909120 MtrunA17_Chr8g0355771 79.688 64 13 0 1 64 1 64 1.37e-32 109
Msa0909120 MtrunA17_Chr8g0355641 71.875 64 18 0 1 64 1 64 8.93e-30 102
Msa0909120 MtrunA17_Chr8g0355761 70.312 64 19 0 1 64 1 64 3.08e-29 101
Msa0909120 MtrunA17_Chr8g0355781 68.750 64 20 0 1 64 1 64 1.00e-28 99.8
Msa0909120 MtrunA17_Chr1g0160381 40.625 64 37 1 1 64 5 67 4.71e-14 62.4
Msa0909120 MtrunA17_Chr1g0160371 42.188 64 36 1 1 64 1 63 5.36e-13 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 12 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTCACCTTCATGAAGTT+TGG 0.292428 6_2:+10308852 None:intergenic
CATTCAGAAATGGTGCTTGC+TGG 0.350620 6_2:-10308982 None:intergenic
TTGTGCAGATGGAGGATCTA+TGG 0.374429 6_2:-10308551 Msa0909120:intron
AAACACTGGACTTATGTCAT+AGG 0.490184 6_2:-10308808 Msa0909120:intron
AACTTCATGAAGGTGAAGAT+TGG 0.494334 6_2:-10308849 Msa0909120:CDS
AGTTTGAAGAACTTGTCAAC+GGG 0.511180 6_2:+10308928 None:intergenic
GGTAAACTTAGTACTGAACT+TGG 0.538495 6_2:-10308961 Msa0909120:CDS
CATCATGCCAAACTTCATGA+AGG 0.593864 6_2:-10308859 Msa0909120:CDS
TAGTTTGAAGAACTTGTCAA+CGG 0.601012 6_2:+10308927 None:intergenic
GTAAACTTAGTACTGAACTT+GGG 0.614711 6_2:-10308960 Msa0909120:CDS
ACACTGATTCAGTTAAACAC+TGG 0.620261 6_2:-10308822 Msa0909120:CDS
CAGATGGAGGATCTATGGAG+AGG 0.673249 6_2:-10308546 Msa0909120:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGCTCTTATTAATTGAATTA+AGG + chr6_2:10308823-10308842 None:intergenic 20.0%
!!! AATTCAATTAATAAGAGCAT+AGG - chr6_2:10308824-10308843 Msa0909120:CDS 20.0%
!!! ATTCAATTAATAAGAGCATA+GGG - chr6_2:10308825-10308844 Msa0909120:CDS 20.0%
!! CATAATCTTCGTATAAAATA+TGG + chr6_2:10308852-10308871 None:intergenic 20.0%
! AAATAAACAAGATGATGACT+TGG + chr6_2:10308760-10308779 None:intergenic 25.0%
! ACTTTATCTTTGTCATCTTT+AGG + chr6_2:10308876-10308895 None:intergenic 25.0%
! GTAAACTTAGTACTGAACTT+GGG - chr6_2:10308550-10308569 Msa0909120:intron 30.0%
TAGTTTGAAGAACTTGTCAA+CGG + chr6_2:10308586-10308605 None:intergenic 30.0%
AAAAATAAGACACTGTTTCC+TGG - chr6_2:10308922-10308941 Msa0909120:CDS 30.0%
ACAAATTCATATATGATGCC+AGG + chr6_2:10308943-10308962 None:intergenic 30.0%
CATATATGAATTTGTGCAGA+TGG - chr6_2:10308948-10308967 Msa0909120:CDS 30.0%
! GGTAAACTTAGTACTGAACT+TGG - chr6_2:10308549-10308568 Msa0909120:intron 35.0%
AGTTTGAAGAACTTGTCAAC+GGG + chr6_2:10308585-10308604 None:intergenic 35.0%
ATCTTCACCTTCATGAAGTT+TGG + chr6_2:10308661-10308680 None:intergenic 35.0%
AACTTCATGAAGGTGAAGAT+TGG - chr6_2:10308661-10308680 Msa0909120:intron 35.0%
!! ACACTGATTCAGTTAAACAC+TGG - chr6_2:10308688-10308707 Msa0909120:intron 35.0%
AAACACTGGACTTATGTCAT+AGG - chr6_2:10308702-10308721 Msa0909120:intron 35.0%
!! AAGATGATGACTTGGTTATG+AGG + chr6_2:10308752-10308771 None:intergenic 35.0%
ATATGAATTTGTGCAGATGG+AGG - chr6_2:10308951-10308970 Msa0909120:CDS 35.0%
CATCATGCCAAACTTCATGA+AGG - chr6_2:10308651-10308670 Msa0909120:intron 40.0%
TTGTGCAGATGGAGGATCTA+TGG - chr6_2:10308959-10308978 Msa0909120:CDS 45.0%
CAGATGGAGGATCTATGGAG+AGG - chr6_2:10308964-10308983 Msa0909120:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 10308537 10308995 10308537 ID=Msa0909120;Name=Msa0909120
chr6_2 mRNA 10308537 10308995 10308537 ID=Msa0909120-mRNA-1;Parent=Msa0909120;Name=Msa0909120-mRNA-1;_AED=0.54;_eAED=0.54;_QI=0|0|0|0.5|1|1|2|0|71
chr6_2 exon 10308809 10308995 10308809 ID=Msa0909120-mRNA-1:exon:2666;Parent=Msa0909120-mRNA-1
chr6_2 exon 10308537 10308565 10308537 ID=Msa0909120-mRNA-1:exon:2665;Parent=Msa0909120-mRNA-1
chr6_2 CDS 10308809 10308995 10308809 ID=Msa0909120-mRNA-1:cds;Parent=Msa0909120-mRNA-1
chr6_2 CDS 10308537 10308565 10308537 ID=Msa0909120-mRNA-1:cds;Parent=Msa0909120-mRNA-1
Gene Sequence

>Msa0909120

ATGGTGCTTGCTGGTAAACTTAGTACTGAACTTGGGATCAAAACACCCGTTGACAAGTTCTTCAAACTATATGCATCAGAACTTCACGAAGTGCAAAACATTAGTGAAAGAATTCATCATGCCAAACTTCATGAAGGTGAAGATTGGCATCACACTGATTCAGTTAAACACTGGACTTATGTCATAGATGGAGGATCTATGGAGAGGAAAAGATAA

Protein sequence

>Msa0909120

MVLAGKLSTELGIKTPVDKFFKLYASELHEVQNISERIHHAKLHEGEDWHHTDSVKHWTYVIDGGSMERKR*