AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0950640

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0950640 MtrunA17_Chr2g0281511 48.333 120 25 1 1 83 1 120 4.93e-33 110
Msa0950640 MtrunA17_Chr2g0309121 46.218 119 28 1 1 83 1 119 4.77e-31 105
Msa0950640 MtrunA17_Chr5g0430431 40.909 66 38 1 14 79 190 254 2.23e-13 62.8
Msa0950640 MtrunA17_Chr7g0276661 39.655 58 34 1 25 82 110 166 2.11e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 7 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGTCAATAATCATCCTAAT+AGG 0.345853 6_3:+39292903 Msa0950640:CDS
ACAGTAGCATACATCCTATT+AGG 0.371456 6_3:-39292917 None:intergenic
GTACGACTTTATTCTTGAAA+AGG 0.406390 6_3:+39292850 Msa0950640:CDS
TACGACTTTATTCTTGAAAA+GGG 0.472985 6_3:+39292851 Msa0950640:CDS
CTTGAAAAGGGCCTAAAAGT+TGG 0.485462 6_3:+39292863 Msa0950640:CDS
GACATTGGAGTTGAAGTCAA+TGG 0.562356 6_3:+39292493 Msa0950640:CDS
TTTATGCATGGTTCTTGACG+CGG 0.664765 6_3:-39292807 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAATGTTAATGTTTCTAGTT+TGG + chr6_3:39292566-39292585 Msa0950640:intron 20.0%
! ACCATGCATAAAAAATACAT+AGG + chr6_3:39292818-39292837 Msa0950640:CDS 25.0%
! CCATGCATAAAAAATACATA+GGG + chr6_3:39292819-39292838 Msa0950640:CDS 25.0%
! TACGACTTTATTCTTGAAAA+GGG + chr6_3:39292851-39292870 Msa0950640:CDS 25.0%
!! GTTAATGTTTCTAGTTTGGA+TGG + chr6_3:39292570-39292589 Msa0950640:intron 30.0%
TACCAGTTTCTTCATCAAAA+AGG - chr6_3:39292763-39292782 None:intergenic 30.0%
!!! CCCTATGTATTTTTTATGCA+TGG - chr6_3:39292822-39292841 None:intergenic 30.0%
CATAAAAAATACATAGGGAG+AGG + chr6_3:39292824-39292843 Msa0950640:CDS 30.0%
GTACGACTTTATTCTTGAAA+AGG + chr6_3:39292850-39292869 Msa0950640:CDS 30.0%
! AAATAACGTCACCAACTTTT+AGG - chr6_3:39292877-39292896 None:intergenic 30.0%
! CTCCTTTTTGATGAAGAAAC+TGG + chr6_3:39292758-39292777 Msa0950640:intron 35.0%
AAAAATACATAGGGAGAGGA+TGG + chr6_3:39292828-39292847 Msa0950640:CDS 35.0%
!! TGGTGACGTTATTTTGTTCA+CGG + chr6_3:39292883-39292902 Msa0950640:CDS 35.0%
CGGTCAATAATCATCCTAAT+AGG + chr6_3:39292903-39292922 Msa0950640:CDS 35.0%
ACAGTAGCATACATCCTATT+AGG - chr6_3:39292920-39292939 None:intergenic 35.0%
GACATTGGAGTTGAAGTCAA+TGG + chr6_3:39292493-39292512 Msa0950640:CDS 40.0%
! TCTAGTTTGGATGGAAACAG+TGG + chr6_3:39292579-39292598 Msa0950640:intron 40.0%
TTTGGATGGAAACAGTGGTT+TGG + chr6_3:39292584-39292603 Msa0950640:intron 40.0%
TTTATGCATGGTTCTTGACG+CGG - chr6_3:39292810-39292829 None:intergenic 40.0%
CTTGAAAAGGGCCTAAAAGT+TGG + chr6_3:39292863-39292882 Msa0950640:CDS 40.0%
!! GGAAACAGTGGTTTGGTTAG+TGG + chr6_3:39292591-39292610 Msa0950640:intron 45.0%
! TCCTCAACGTTTGCTGAGAG+TGG + chr6_3:39292710-39292729 Msa0950640:intron 50.0%
ACCACTCTCAGCAAACGTTG+AGG - chr6_3:39292714-39292733 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 39292487 39292949 39292487 ID=Msa0950640;Name=Msa0950640
chr6_3 mRNA 39292487 39292949 39292487 ID=Msa0950640-mRNA-1;Parent=Msa0950640;Name=Msa0950640-mRNA-1;_AED=0.18;_eAED=0.30;_QI=0|0|0|1|0|0|2|0|83
chr6_3 exon 39292487 39292562 39292487 ID=Msa0950640-mRNA-1:exon:9535;Parent=Msa0950640-mRNA-1
chr6_3 exon 39292774 39292949 39292774 ID=Msa0950640-mRNA-1:exon:9536;Parent=Msa0950640-mRNA-1
chr6_3 CDS 39292487 39292562 39292487 ID=Msa0950640-mRNA-1:cds;Parent=Msa0950640-mRNA-1
chr6_3 CDS 39292774 39292949 39292774 ID=Msa0950640-mRNA-1:cds;Parent=Msa0950640-mRNA-1
Gene Sequence

>Msa0950640

ATGAATGACATTGGAGTTGAAGTCAATGGTAGTGAATTAGAGAAAATGTTCAAAATGTCGATGTTCATTATTGAAAAAACTGGTAAATCTTATGAATGTGATGTTCACACCGCGTCAAGAACCATGCATAAAAAATACATAGGGAGAGGATGGTACGACTTTATTCTTGAAAAGGGCCTAAAAGTTGGTGACGTTATTTTGTTCACGGTCAATAATCATCCTAATAGGATGTATGCTACTGTCGTTAACTGA
Protein sequence

>Msa0950640

MNDIGVEVNGSELEKMFKMSMFIIEKTGKSYECDVHTASRTMHKKYIGRGWYDFILEKGLKVGDVILFTVNNHPNRMYATVVN*