AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1345240

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1345240 MtrunA17_Chr7g0233141 79.710 69 13 1 1 69 160 227 8.07e-32 112
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCTTCCTCACTCTCTTTC+TGG 0.024047 tig0007112:-82850 Msa1345240:CDS
CCATTCTCCACGGTCATTTC+AGG 0.178622 tig0007112:-82944 Msa1345240:CDS
CCCTATCATCATTGCCTTGC+CGG 0.232397 tig0007112:-82969 Msa1345240:CDS
TGCTTCCTCACTCTCTTTCT+GGG 0.299616 tig0007112:-82849 Msa1345240:CDS
ATTGGCCACCCTCCACAAAA+TGG 0.374108 tig0007112:+82897 None:intergenic
TGTCACTCTACTTCAAGTTA+TGG 0.389092 tig0007112:-82760 Msa1345240:CDS
CCCGGCAAGGCAATGATGAT+AGG 0.402119 tig0007112:+82968 None:intergenic
GTCACTCTACTTCAAGTTAT+GGG 0.417255 tig0007112:-82759 Msa1345240:CDS
CGAAGAAGAAGTCAAGGTTC+AGG 0.440816 tig0007112:-83041 Msa1345240:CDS
TCATTTCAGGATTCTGCTGT+TGG 0.441223 tig0007112:-82931 Msa1345240:CDS
CCTGAAATGACCGTGGAGAA+TGG 0.455573 tig0007112:+82944 None:intergenic
CCTATCATCATTGCCTTGCC+GGG 0.458752 tig0007112:-82968 Msa1345240:CDS
TACTTCAAGTTATGGGATCC+TGG 0.483010 tig0007112:-82752 Msa1345240:CDS
TGAAGTAGAGTGACAGATCA+AGG 0.511014 tig0007112:+82768 None:intergenic
CAAAACAGAGTGTATGATCC+AGG 0.512776 tig0007112:-82812 Msa1345240:CDS
GGATAACATAAGTGTCCTCC+AGG 0.530824 tig0007112:+82734 None:intergenic
CCGGCAAGGCAATGATGATA+GGG 0.535016 tig0007112:+82969 None:intergenic
TCAGGATGCAGAAAAGATGA+AGG 0.538842 tig0007112:-83023 Msa1345240:CDS
ACCCTCCACAAAATGGTTGT+CGG 0.547468 tig0007112:+82904 None:intergenic
TTATGTTATCCTTCACCTTG+AGG 0.548558 tig0007112:-82722 None:intergenic
TGATGATAGGGCGAACACTA+AGG 0.563068 tig0007112:+82981 None:intergenic
CGTGGAGAATGGACCCGGCA+AGG 0.569156 tig0007112:+82955 None:intergenic
GGAGCATGAAAACATATGCC+TGG 0.570100 tig0007112:+82794 None:intergenic
ATGACCGTGGAGAATGGACC+CGG 0.580029 tig0007112:+82950 None:intergenic
TCACCTTGTCCTCAAGGTGA+AGG 0.591944 tig0007112:+82713 None:intergenic
CTTGCCGGGTCCATTCTCCA+CGG 0.592362 tig0007112:-82954 Msa1345240:CDS
TTTGGCCCAGAAAGAGAGTG+AGG 0.592737 tig0007112:+82844 None:intergenic
CAGGATGCAGAAAAGATGAA+GGG 0.616929 tig0007112:-83022 Msa1345240:CDS
AAAGAGAGTGAGGAAGCAGT+AGG 0.627649 tig0007112:+82854 None:intergenic
AGATGTCGAAGAAGAAGTCA+AGG 0.631739 tig0007112:-83047 Msa1345240:CDS
AGGATGCAGAAAAGATGAAG+GGG 0.649303 tig0007112:-83021 Msa1345240:CDS
TAGAGTGACAGATCAAGGTG+TGG 0.659701 tig0007112:+82773 None:intergenic
GCAGAATCCTGAAATGACCG+TGG 0.690411 tig0007112:+82937 None:intergenic
GGATGCAGAAAAGATGAAGG+GGG 0.706575 tig0007112:-83020 Msa1345240:CDS
GAACACTAAGGTTCACAGCG+AGG 0.713156 tig0007112:+82993 None:intergenic
TTCAAGTTATGGGATCCTGG+AGG 0.737576 tig0007112:-82749 Msa1345240:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTGTTTTGAGTAGTATTTT+TGG + tig0007112:82965-82984 None:intergenic 25.0%
! TTTTCTCCATCAAAAGACAT+TGG + tig0007112:82912-82931 None:intergenic 30.0%
! AATGTCTTTTGATGGAGAAA+AGG - tig0007112:82911-82930 Msa1345240:CDS 30.0%
! TGTCACTCTACTTCAAGTTA+TGG - tig0007112:83028-83047 Msa1345240:CDS 35.0%
! GTCACTCTACTTCAAGTTAT+GGG - tig0007112:83029-83048 Msa1345240:CDS 35.0%
AGATGTCGAAGAAGAAGTCA+AGG - tig0007112:82741-82760 Msa1345240:CDS 40.0%
TCAGGATGCAGAAAAGATGA+AGG - tig0007112:82765-82784 Msa1345240:CDS 40.0%
CAGGATGCAGAAAAGATGAA+GGG - tig0007112:82766-82785 Msa1345240:CDS 40.0%
AGGATGCAGAAAAGATGAAG+GGG - tig0007112:82767-82786 Msa1345240:CDS 40.0%
TCATTTCAGGATTCTGCTGT+TGG - tig0007112:82857-82876 Msa1345240:CDS 40.0%
! GAATTCCGACAACCATTTTG+TGG - tig0007112:82879-82898 Msa1345240:CDS 40.0%
CAAAACAGAGTGTATGATCC+AGG - tig0007112:82976-82995 Msa1345240:CDS 40.0%
TGAAGTAGAGTGACAGATCA+AGG + tig0007112:83023-83042 None:intergenic 40.0%
! TACTTCAAGTTATGGGATCC+TGG - tig0007112:83036-83055 Msa1345240:CDS 40.0%
CGAAGAAGAAGTCAAGGTTC+AGG - tig0007112:82747-82766 Msa1345240:CDS 45.0%
GGATGCAGAAAAGATGAAGG+GGG - tig0007112:82768-82787 Msa1345240:CDS 45.0%
TGATGATAGGGCGAACACTA+AGG + tig0007112:82810-82829 None:intergenic 45.0%
! TTCCGACAACCATTTTGTGG+AGG - tig0007112:82882-82901 Msa1345240:CDS 45.0%
! TCCGACAACCATTTTGTGGA+GGG - tig0007112:82883-82902 Msa1345240:CDS 45.0%
ACCCTCCACAAAATGGTTGT+CGG + tig0007112:82887-82906 None:intergenic 45.0%
AAAGAGAGTGAGGAAGCAGT+AGG + tig0007112:82937-82956 None:intergenic 45.0%
TGCTTCCTCACTCTCTTTCT+GGG - tig0007112:82939-82958 Msa1345240:CDS 45.0%
GGAGCATGAAAACATATGCC+TGG + tig0007112:82997-83016 None:intergenic 45.0%
TAGAGTGACAGATCAAGGTG+TGG + tig0007112:83018-83037 None:intergenic 45.0%
! TTCAAGTTATGGGATCCTGG+AGG - tig0007112:83039-83058 Msa1345240:CDS 45.0%
GGATAACATAAGTGTCCTCC+AGG + tig0007112:83057-83076 None:intergenic 45.0%
GAACACTAAGGTTCACAGCG+AGG + tig0007112:82798-82817 None:intergenic 50.0%
CCGGCAAGGCAATGATGATA+GGG + tig0007112:82822-82841 None:intergenic 50.0%
CCCTATCATCATTGCCTTGC+CGG - tig0007112:82819-82838 Msa1345240:CDS 50.0%
CCTATCATCATTGCCTTGCC+GGG - tig0007112:82820-82839 Msa1345240:CDS 50.0%
CCTGAAATGACCGTGGAGAA+TGG + tig0007112:82847-82866 None:intergenic 50.0%
CCATTCTCCACGGTCATTTC+AGG - tig0007112:82844-82863 Msa1345240:CDS 50.0%
GCAGAATCCTGAAATGACCG+TGG + tig0007112:82854-82873 None:intergenic 50.0%
! GACAACCATTTTGTGGAGGG+TGG - tig0007112:82886-82905 Msa1345240:CDS 50.0%
ATTGGCCACCCTCCACAAAA+TGG + tig0007112:82894-82913 None:intergenic 50.0%
! GGGTGGCCAATGTCTTTTGA+TGG - tig0007112:82903-82922 Msa1345240:CDS 50.0%
CTGCTTCCTCACTCTCTTTC+TGG - tig0007112:82938-82957 Msa1345240:CDS 50.0%
TTTGGCCCAGAAAGAGAGTG+AGG + tig0007112:82947-82966 None:intergenic 50.0%
CCCGGCAAGGCAATGATGAT+AGG + tig0007112:82823-82842 None:intergenic 55.0%
ATGACCGTGGAGAATGGACC+CGG + tig0007112:82841-82860 None:intergenic 55.0%
CTTGCCGGGTCCATTCTCCA+CGG - tig0007112:82834-82853 Msa1345240:CDS 60.0%
CGTGGAGAATGGACCCGGCA+AGG + tig0007112:82836-82855 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0007112 gene 82724 83086 82724 ID=Msa1345240;Name=Msa1345240
tig0007112 mRNA 82724 83086 82724 ID=Msa1345240-mRNA-1;Parent=Msa1345240;Name=Msa1345240-mRNA-1;_AED=0.56;_eAED=0.56;_QI=0|-1|0|1|-1|1|1|0|120
tig0007112 exon 82724 83086 82724 ID=Msa1345240-mRNA-1:exon:4903;Parent=Msa1345240-mRNA-1
tig0007112 CDS 82724 83086 82724 ID=Msa1345240-mRNA-1:cds;Parent=Msa1345240-mRNA-1
Gene Sequence

>Msa1345240

ATGACGGTTATCGATGAAGATGTCGAAGAAGAAGTCAAGGTTCAGGATGCAGAAAAGATGAAGGGGGAGTTCCTCGCTGTGAACCTTAGTGTTCGCCCTATCATCATTGCCTTGCCGGGTCCATTCTCCACGGTCATTTCAGGATTCTGCTGTTGGAATTCCGACAACCATTTTGTGGAGGGTGGCCAATGTCTTTTGATGGAGAAAAGGCCTACTGCTTCCTCACTCTCTTTCTGGGCCAAAAATACTACTCAAAACAGAGTGTATGATCCAGGCATATGTTTTCATGCTCCACACCTTGATCTGTCACTCTACTTCAAGTTATGGGATCCTGGAGGACACTTATGTTATCCTTCACCTTGA
Protein sequence

>Msa1345240

MTVIDEDVEEEVKVQDAEKMKGEFLAVNLSVRPIIIALPGPFSTVISGFCCWNSDNHFVEGGQCLLMEKRPTASSLSFWAKNTTQNRVYDPGICFHAPHLDLSLYFKLWDPGGHLCYPSP*