AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0954040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0954040 MtrunA17_Chr5g0393501 28.916 166 97 3 2 146 76 241 1.47e-18 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAAGTTCCTATCTGGATA+TGG 0.289906 6_3:+53012568 Msa0954040:intron
GTACCTTTGAAGTTCCTATC+TGG 0.333773 6_3:+53012562 Msa0954040:intron
AATCGTGATGTTTCACTCTA+AGG 0.341127 6_3:-53012734 None:intergenic
AGGAATTTGCCGAATGTATC+AGG 0.344712 6_3:-53012714 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 6_3:-53012455 None:intergenic
TCCGAACATCACATTTCGTA+TGG 0.444579 6_3:-53012820 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 6_3:+53012860 Msa0954040:CDS
CGAAATGTGATGTTCGGAAA+AGG 0.465930 6_3:+53012825 Msa0954040:CDS
CCCATACGAAATGTGATGTT+CGG 0.471184 6_3:+53012819 Msa0954040:CDS
TAGGAACTACCTGATACATT+CGG 0.475748 6_3:+53012705 Msa0954040:intron
TGCCACACTCATGGAATGAT+AGG 0.480870 6_3:-53012526 None:intergenic
TCGTCGATCCATATCCAGAT+AGG 0.486078 6_3:-53012576 None:intergenic
GGCCGTTGTTGACAGATGGT+TGG 0.487397 6_3:+53012382 Msa0954040:CDS
GTCATGCGTTTATCAACGCT+TGG 0.494559 6_3:-53012943 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 6_3:+53012861 Msa0954040:CDS
CCGAACATCACATTTCGTAT+GGG 0.503117 6_3:-53012819 None:intergenic
ATTATTGCTTTCCAGTACCT+TGG 0.503165 6_3:+53012444 Msa0954040:CDS
ACACGATGTTGCCACACTCA+TGG 0.518160 6_3:-53012535 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.528831 6_3:-53012774 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 6_3:+53012378 Msa0954040:CDS
TGATAGGGTGGATAATCAGC+TGG 0.541144 6_3:-53012510 None:intergenic
CGAACATCACATTTCGTATG+GGG 0.542386 6_3:-53012818 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.543494 6_3:-53012792 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 6_3:+53012447 Msa0954040:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 6_3:-53012868 None:intergenic
CACGATTACGTCATGTTGTG+CGG 0.590860 6_3:+53012750 Msa0954040:CDS
TGTTCAACAAATCAGTTAGT+CGG 0.609582 6_3:+53012361 Msa0954040:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.616153 6_3:+53012829 Msa0954040:CDS
TTTCAAGTGCAAGTGCGTCG+TGG 0.639560 6_3:+53012899 Msa0954040:CDS
GCCACACTCATGGAATGATA+GGG 0.654738 6_3:-53012525 None:intergenic
ACACTCATGGAATGATAGGG+TGG 0.656827 6_3:-53012522 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 6_3:-53012384 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 6_3:-53012461 None:intergenic
TGGATCGACGAAATCACCGA+AGG 0.700849 6_3:+53012588 Msa0954040:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 6_3:+53012864 Msa0954040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACAGTTTTTTTTTCTTTTTT+AGG + chr6_3:53012686-53012705 Msa0954040:intron 15.0%
!! AAAAAACAATAAACAACCTT+CGG - chr6_3:53012607-53012626 None:intergenic 20.0%
!! TTTTGATGCTATTCATTTAG+AGG + chr6_3:53012624-53012643 Msa0954040:intron 25.0%
TGTTCAACAAATCAGTTAGT+CGG + chr6_3:53012361-53012380 Msa0954040:CDS 30.0%
TGATTATTCTACGAGTTTAG+TGG + chr6_3:53012414-53012433 Msa0954040:intron 30.0%
ACAGGAATGATATTGTCATA+AGG - chr6_3:53012777-53012796 None:intergenic 30.0%
ATTATTGCTTTCCAGTACCT+TGG + chr6_3:53012444-53012463 Msa0954040:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr6_3:53012464-53012483 None:intergenic 35.0%
TATCCAGATAGGAACTTCAA+AGG - chr6_3:53012568-53012587 None:intergenic 35.0%
TTGAAGTTCCTATCTGGATA+TGG + chr6_3:53012568-53012587 Msa0954040:intron 35.0%
TAGGAACTACCTGATACATT+CGG + chr6_3:53012705-53012724 Msa0954040:intron 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr6_3:53012737-53012756 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr6_3:53012795-53012814 None:intergenic 35.0%
!! GTACCTTTGAAGTTCCTATC+TGG + chr6_3:53012562-53012581 Msa0954040:intron 40.0%
AGGAATTTGCCGAATGTATC+AGG - chr6_3:53012717-53012736 None:intergenic 40.0%
CGAACATCACATTTCGTATG+GGG - chr6_3:53012821-53012840 None:intergenic 40.0%
CCGAACATCACATTTCGTAT+GGG - chr6_3:53012822-53012841 None:intergenic 40.0%
CCCATACGAAATGTGATGTT+CGG + chr6_3:53012819-53012838 Msa0954040:CDS 40.0%
TCCGAACATCACATTTCGTA+TGG - chr6_3:53012823-53012842 None:intergenic 40.0%
CGAAATGTGATGTTCGGAAA+AGG + chr6_3:53012825-53012844 Msa0954040:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr6_3:53012829-53012848 Msa0954040:CDS 40.0%
CTCCAACCATCTGTCAACAA+CGG - chr6_3:53012387-53012406 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr6_3:53012447-53012466 Msa0954040:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr6_3:53012458-53012477 None:intergenic 45.0%
TGATAGGGTGGATAATCAGC+TGG - chr6_3:53012513-53012532 None:intergenic 45.0%
ACACTCATGGAATGATAGGG+TGG - chr6_3:53012525-53012544 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+TGG + chr6_3:53012524-53012543 Msa0954040:intron 45.0%
GCCACACTCATGGAATGATA+GGG - chr6_3:53012528-53012547 None:intergenic 45.0%
TGCCACACTCATGGAATGAT+AGG - chr6_3:53012529-53012548 None:intergenic 45.0%
TCGTCGATCCATATCCAGAT+AGG - chr6_3:53012579-53012598 None:intergenic 45.0%
CACGATTACGTCATGTTGTG+CGG + chr6_3:53012750-53012769 Msa0954040:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr6_3:53012852-53012871 Msa0954040:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr6_3:53012860-53012879 Msa0954040:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr6_3:53012861-53012880 Msa0954040:CDS 45.0%
ACACGATGTTGCCACACTCA+TGG - chr6_3:53012538-53012557 None:intergenic 50.0%
TGGATCGACGAAATCACCGA+AGG + chr6_3:53012588-53012607 Msa0954040:CDS 50.0%
! TTTCAAGTGCAAGTGCGTCG+TGG + chr6_3:53012899-53012918 Msa0954040:CDS 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr6_3:53012378-53012397 Msa0954040:CDS 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr6_3:53012382-53012401 Msa0954040:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr6_3:53012864-53012883 Msa0954040:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr6_3:53012871-53012890 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 53012360 53012953 53012360 ID=Msa0954040;Name=Msa0954040
chr6_3 mRNA 53012360 53012953 53012360 ID=Msa0954040-mRNA-1;Parent=Msa0954040;Name=Msa0954040-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|0.33|0|1|0.33|0.5|4|0|147
chr6_3 exon 53012360 53012412 53012360 ID=Msa0954040-mRNA-1:exon:11144;Parent=Msa0954040-mRNA-1
chr6_3 exon 53012434 53012542 53012434 ID=Msa0954040-mRNA-1:exon:11145;Parent=Msa0954040-mRNA-1
chr6_3 exon 53012574 53012609 53012574 ID=Msa0954040-mRNA-1:exon:11146;Parent=Msa0954040-mRNA-1
chr6_3 exon 53012708 53012953 53012708 ID=Msa0954040-mRNA-1:exon:11147;Parent=Msa0954040-mRNA-1
chr6_3 CDS 53012360 53012412 53012360 ID=Msa0954040-mRNA-1:cds;Parent=Msa0954040-mRNA-1
chr6_3 CDS 53012434 53012542 53012434 ID=Msa0954040-mRNA-1:cds;Parent=Msa0954040-mRNA-1
chr6_3 CDS 53012574 53012609 53012574 ID=Msa0954040-mRNA-1:cds;Parent=Msa0954040-mRNA-1
chr6_3 CDS 53012708 53012953 53012708 ID=Msa0954040-mRNA-1:cds;Parent=Msa0954040-mRNA-1
Gene Sequence

>Msa0954040

ATGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACGTTACTCCAGCTGATTATCCACCCTATCATTCCATGAGTTTCCTATCTGGATATGGATCGACGAAATCACCGAAGGAACTACCTGATACATTCGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTGCGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGATGACCCCATACGAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCGTGGACAAAAAATATGTTATCGTATCCAAGCGTTGA
Protein sequence

>Msa0954040

MFNKSVSRPLLTDGWSAFGSKIIAFQYLGGSRFQIFVFAHNVTPADYPPYHSMSFLSGYGSTKSPKELPDTFGKFLRVKHHDYVMLCGPYDNIIPVRLKYTDDPIRNVMFGKGWTSFCAANGIEGGDVLIFKCKCVVDKKYVIVSKR*