AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0466070


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0466070 MtrunA17_Chr3g0118801 96.000 125 5 0 9 133 93 217 7.75e-84 245
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0466070 AT2G21530.1 59.664 119 47 1 9 127 92 209 5.67e-46 149

Find 29 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATCTTCTTGTTATAGATT+TGG 0.263843 3_3:+66629582 Msa0466070:CDS
TCTGGGAGTTATATTACTTT+TGG 0.301923 3_3:+66629670 Msa0466070:CDS
AATGCCAGGGGACACTAATT+TGG 0.313943 3_3:+66629897 Msa0466070:intron
ACTTCTATACCTGTTGCAAC+TGG 0.344018 3_3:-66629365 None:intergenic
CCATTGTCTAGTTCACCTTC+TGG 0.345009 3_3:-66629973 None:intergenic
GTAGTTACCACTGTATCTTC+TGG 0.366490 3_3:+66629652 Msa0466070:CDS
CCATCTCCTATCAAAATGAT+TGG 0.398371 3_3:-66629160 None:intergenic
ATCACTAAATCAGCTTTCTC+TGG 0.443107 3_3:-66629341 None:intergenic
TTAGTGATCCCAGTTGCAAC+AGG 0.462387 3_3:+66629356 Msa0466070:CDS
TTCAAGGCATATAGGCTTCA+AGG 0.462486 3_3:+66629186 Msa0466070:CDS
GATGGTGATTCAAGGCATAT+AGG 0.467110 3_3:+66629178 Msa0466070:CDS
AGCACCAATGGAACATTCAT+TGG 0.469041 3_3:+66629607 Msa0466070:CDS
GAACATTCATTGGTGACAAA+AGG 0.471831 3_3:+66629617 Msa0466070:CDS
TAGTTACCACTGTATCTTCT+GGG 0.476442 3_3:+66629653 Msa0466070:CDS
TGATAGGAGATGGTGATTCA+AGG 0.491582 3_3:+66629170 Msa0466070:CDS
GTCACCAATGAATGTTCCAT+TGG 0.522297 3_3:-66629611 None:intergenic
GAGAAGGCTGCAGATACAGT+TGG 0.528528 3_3:+66629946 Msa0466070:CDS
GGTGACAAAAGGCTGAAACC+TGG 0.545814 3_3:+66629628 Msa0466070:CDS
ATAGATTTGGATAGCACCAA+TGG 0.560750 3_3:+66629595 Msa0466070:CDS
GGCTTCAAGGTTGAGAGACC+AGG 0.565164 3_3:+66629199 Msa0466070:CDS
GATACAGTGGTAACTACTCC+AGG 0.567838 3_3:-66629646 None:intergenic
CTTCTATACCTGTTGCAACT+GGG 0.577256 3_3:-66629364 None:intergenic
CAGGTGTGCATGCACGCATT+CGG 0.581165 3_3:+66629548 Msa0466070:CDS
TGTGTCGAAAATAGAAGAGA+AGG 0.593642 3_3:+66629930 Msa0466070:CDS
ATCTAGAATGAAGTCACTGT+AGG 0.636581 3_3:+66629311 Msa0466070:intron
GATACAGTTGGAGAACCAGA+AGG 0.670779 3_3:+66629958 Msa0466070:CDS
GAAGTAATTTCATAAGCACC+TGG 0.674584 3_3:-66629217 None:intergenic
ATAACTCCCAGAAGATACAG+TGG 0.690459 3_3:-66629659 None:intergenic
CCAGAAGGTGAACTAGACAA+TGG 0.701962 3_3:+66629973 Msa0466070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGTAACTGTAAGAAAAAT+AGG - chr3_3:66629422-66629441 None:intergenic 20.0%
!! ACATAATTATTCAACAGAAA+AGG - chr3_3:66629733-66629752 None:intergenic 20.0%
!!! TATCATTTTGAAATTCTCTT+AGG - chr3_3:66629825-66629844 None:intergenic 20.0%
!! TTTGTAACTGTAAGAAAAAT+AGG - chr3_3:66629422-66629441 None:intergenic 20.0%
!! ACATAATTATTCAACAGAAA+AGG - chr3_3:66629733-66629752 None:intergenic 20.0%
!!! TATCATTTTGAAATTCTCTT+AGG - chr3_3:66629825-66629844 None:intergenic 20.0%
!!! ACAAAACCAATCATTTTGAT+AGG + chr3_3:66629154-66629173 Msa0466070:CDS 25.0%
! AGCATAGTACATTAAGATTA+AGG - chr3_3:66629468-66629487 None:intergenic 25.0%
! CAAATTATATTGTGATTCTC+TGG - chr3_3:66629502-66629521 None:intergenic 25.0%
!! CAATCTTCTTGTTATAGATT+TGG + chr3_3:66629582-66629601 Msa0466070:CDS 25.0%
! TTGAAATTCTCTTAGGAATA+TGG - chr3_3:66629818-66629837 None:intergenic 25.0%
! ATAATAGCAGAGGTTAAATA+TGG - chr3_3:66629876-66629895 None:intergenic 25.0%
!!! ACAAAACCAATCATTTTGAT+AGG + chr3_3:66629154-66629173 Msa0466070:CDS 25.0%
! AGCATAGTACATTAAGATTA+AGG - chr3_3:66629468-66629487 None:intergenic 25.0%
! CAAATTATATTGTGATTCTC+TGG - chr3_3:66629502-66629521 None:intergenic 25.0%
!! CAATCTTCTTGTTATAGATT+TGG + chr3_3:66629582-66629601 Msa0466070:CDS 25.0%
! TTGAAATTCTCTTAGGAATA+TGG - chr3_3:66629818-66629837 None:intergenic 25.0%
! ATAATAGCAGAGGTTAAATA+TGG - chr3_3:66629876-66629895 None:intergenic 25.0%
! ATCAGAATCAATGATTTGTG+TGG + chr3_3:66629250-66629269 Msa0466070:intron 30.0%
! TGTTTTGTATTTACAGTGTC+AGG + chr3_3:66629529-66629548 Msa0466070:intron 30.0%
! TCTGGGAGTTATATTACTTT+TGG + chr3_3:66629670-66629689 Msa0466070:CDS 30.0%
TATATAACCCTGTTTGTAGA+AGG + chr3_3:66629779-66629798 Msa0466070:intron 30.0%
TTAAGATCCTTCTACAAACA+GGG - chr3_3:66629789-66629808 None:intergenic 30.0%
! TTTAAGATCCTTCTACAAAC+AGG - chr3_3:66629790-66629809 None:intergenic 30.0%
CAGAGGTTAAATATGGAATA+GGG - chr3_3:66629869-66629888 None:intergenic 30.0%
! ATCAGAATCAATGATTTGTG+TGG + chr3_3:66629250-66629269 Msa0466070:intron 30.0%
! TGTTTTGTATTTACAGTGTC+AGG + chr3_3:66629529-66629548 Msa0466070:intron 30.0%
! TCTGGGAGTTATATTACTTT+TGG + chr3_3:66629670-66629689 Msa0466070:CDS 30.0%
TATATAACCCTGTTTGTAGA+AGG + chr3_3:66629779-66629798 Msa0466070:intron 30.0%
TTAAGATCCTTCTACAAACA+GGG - chr3_3:66629789-66629808 None:intergenic 30.0%
! TTTAAGATCCTTCTACAAAC+AGG - chr3_3:66629790-66629809 None:intergenic 30.0%
CAGAGGTTAAATATGGAATA+GGG - chr3_3:66629869-66629888 None:intergenic 30.0%
CCATCTCCTATCAAAATGAT+TGG - chr3_3:66629163-66629182 None:intergenic 35.0%
!! CCAATCATTTTGATAGGAGA+TGG + chr3_3:66629160-66629179 Msa0466070:CDS 35.0%
GAAGTAATTTCATAAGCACC+TGG - chr3_3:66629220-66629239 None:intergenic 35.0%
! ATCTAGAATGAAGTCACTGT+AGG + chr3_3:66629311-66629330 Msa0466070:intron 35.0%
ATCACTAAATCAGCTTTCTC+TGG - chr3_3:66629344-66629363 None:intergenic 35.0%
GATTAAGGAGCTTATTTCAG+TGG - chr3_3:66629453-66629472 None:intergenic 35.0%
ATAGATTTGGATAGCACCAA+TGG + chr3_3:66629595-66629614 Msa0466070:CDS 35.0%
! GAACATTCATTGGTGACAAA+AGG + chr3_3:66629617-66629636 Msa0466070:CDS 35.0%
TAGTTACCACTGTATCTTCT+GGG + chr3_3:66629653-66629672 Msa0466070:CDS 35.0%
GCAGAGGTTAAATATGGAAT+AGG - chr3_3:66629870-66629889 None:intergenic 35.0%
! TCTCTTCTATTTTCGACACA+CGG - chr3_3:66629930-66629949 None:intergenic 35.0%
TGTGTCGAAAATAGAAGAGA+AGG + chr3_3:66629930-66629949 Msa0466070:CDS 35.0%
CCATCTCCTATCAAAATGAT+TGG - chr3_3:66629163-66629182 None:intergenic 35.0%
!! CCAATCATTTTGATAGGAGA+TGG + chr3_3:66629160-66629179 Msa0466070:CDS 35.0%
GAAGTAATTTCATAAGCACC+TGG - chr3_3:66629220-66629239 None:intergenic 35.0%
! ATCTAGAATGAAGTCACTGT+AGG + chr3_3:66629311-66629330 Msa0466070:intron 35.0%
ATCACTAAATCAGCTTTCTC+TGG - chr3_3:66629344-66629363 None:intergenic 35.0%
GATTAAGGAGCTTATTTCAG+TGG - chr3_3:66629453-66629472 None:intergenic 35.0%
ATAGATTTGGATAGCACCAA+TGG + chr3_3:66629595-66629614 Msa0466070:CDS 35.0%
! GAACATTCATTGGTGACAAA+AGG + chr3_3:66629617-66629636 Msa0466070:CDS 35.0%
TAGTTACCACTGTATCTTCT+GGG + chr3_3:66629653-66629672 Msa0466070:CDS 35.0%
GCAGAGGTTAAATATGGAAT+AGG - chr3_3:66629870-66629889 None:intergenic 35.0%
! TCTCTTCTATTTTCGACACA+CGG - chr3_3:66629930-66629949 None:intergenic 35.0%
TGTGTCGAAAATAGAAGAGA+AGG + chr3_3:66629930-66629949 Msa0466070:CDS 35.0%
TGATAGGAGATGGTGATTCA+AGG + chr3_3:66629170-66629189 Msa0466070:CDS 40.0%
GATGGTGATTCAAGGCATAT+AGG + chr3_3:66629178-66629197 Msa0466070:CDS 40.0%
TTCAAGGCATATAGGCTTCA+AGG + chr3_3:66629186-66629205 Msa0466070:CDS 40.0%
CTTCTATACCTGTTGCAACT+GGG - chr3_3:66629367-66629386 None:intergenic 40.0%
ACTTCTATACCTGTTGCAAC+TGG - chr3_3:66629368-66629387 None:intergenic 40.0%
AGCACCAATGGAACATTCAT+TGG + chr3_3:66629607-66629626 Msa0466070:CDS 40.0%
GTCACCAATGAATGTTCCAT+TGG - chr3_3:66629614-66629633 None:intergenic 40.0%
GTAGTTACCACTGTATCTTC+TGG + chr3_3:66629652-66629671 Msa0466070:CDS 40.0%
ATAACTCCCAGAAGATACAG+TGG - chr3_3:66629662-66629681 None:intergenic 40.0%
CTCTGCTATTATGAATGCCA+GGG + chr3_3:66629884-66629903 Msa0466070:intron 40.0%
TCTGCTATTATGAATGCCAG+GGG + chr3_3:66629885-66629904 Msa0466070:intron 40.0%
TGATAGGAGATGGTGATTCA+AGG + chr3_3:66629170-66629189 Msa0466070:CDS 40.0%
GATGGTGATTCAAGGCATAT+AGG + chr3_3:66629178-66629197 Msa0466070:CDS 40.0%
TTCAAGGCATATAGGCTTCA+AGG + chr3_3:66629186-66629205 Msa0466070:CDS 40.0%
CTTCTATACCTGTTGCAACT+GGG - chr3_3:66629367-66629386 None:intergenic 40.0%
ACTTCTATACCTGTTGCAAC+TGG - chr3_3:66629368-66629387 None:intergenic 40.0%
AGCACCAATGGAACATTCAT+TGG + chr3_3:66629607-66629626 Msa0466070:CDS 40.0%
GTCACCAATGAATGTTCCAT+TGG - chr3_3:66629614-66629633 None:intergenic 40.0%
GTAGTTACCACTGTATCTTC+TGG + chr3_3:66629652-66629671 Msa0466070:CDS 40.0%
ATAACTCCCAGAAGATACAG+TGG - chr3_3:66629662-66629681 None:intergenic 40.0%
CTCTGCTATTATGAATGCCA+GGG + chr3_3:66629884-66629903 Msa0466070:intron 40.0%
TCTGCTATTATGAATGCCAG+GGG + chr3_3:66629885-66629904 Msa0466070:intron 40.0%
TTAGTGATCCCAGTTGCAAC+AGG + chr3_3:66629356-66629375 Msa0466070:CDS 45.0%
GATACAGTGGTAACTACTCC+AGG - chr3_3:66629649-66629668 None:intergenic 45.0%
CCTGGCATTCATAATAGCAG+AGG - chr3_3:66629886-66629905 None:intergenic 45.0%
CCTCTGCTATTATGAATGCC+AGG + chr3_3:66629883-66629902 Msa0466070:intron 45.0%
AATGCCAGGGGACACTAATT+TGG + chr3_3:66629897-66629916 Msa0466070:intron 45.0%
ATAGCCAAATTAGTGTCCCC+TGG - chr3_3:66629904-66629923 None:intergenic 45.0%
GATACAGTTGGAGAACCAGA+AGG + chr3_3:66629958-66629977 Msa0466070:CDS 45.0%
! CCATTGTCTAGTTCACCTTC+TGG - chr3_3:66629976-66629995 None:intergenic 45.0%
CCAGAAGGTGAACTAGACAA+TGG + chr3_3:66629973-66629992 Msa0466070:CDS 45.0%
TTAGTGATCCCAGTTGCAAC+AGG + chr3_3:66629356-66629375 Msa0466070:CDS 45.0%
GATACAGTGGTAACTACTCC+AGG - chr3_3:66629649-66629668 None:intergenic 45.0%
CCTGGCATTCATAATAGCAG+AGG - chr3_3:66629886-66629905 None:intergenic 45.0%
CCTCTGCTATTATGAATGCC+AGG + chr3_3:66629883-66629902 Msa0466070:intron 45.0%
AATGCCAGGGGACACTAATT+TGG + chr3_3:66629897-66629916 Msa0466070:intron 45.0%
ATAGCCAAATTAGTGTCCCC+TGG - chr3_3:66629904-66629923 None:intergenic 45.0%
GATACAGTTGGAGAACCAGA+AGG + chr3_3:66629958-66629977 Msa0466070:CDS 45.0%
! CCATTGTCTAGTTCACCTTC+TGG - chr3_3:66629976-66629995 None:intergenic 45.0%
CCAGAAGGTGAACTAGACAA+TGG + chr3_3:66629973-66629992 Msa0466070:CDS 45.0%
GGTGACAAAAGGCTGAAACC+TGG + chr3_3:66629628-66629647 Msa0466070:CDS 50.0%
GAGAAGGCTGCAGATACAGT+TGG + chr3_3:66629946-66629965 Msa0466070:CDS 50.0%
GGTGACAAAAGGCTGAAACC+TGG + chr3_3:66629628-66629647 Msa0466070:CDS 50.0%
GAGAAGGCTGCAGATACAGT+TGG + chr3_3:66629946-66629965 Msa0466070:CDS 50.0%
GGCTTCAAGGTTGAGAGACC+AGG + chr3_3:66629199-66629218 Msa0466070:CDS 55.0%
CAGGTGTGCATGCACGCATT+CGG + chr3_3:66629548-66629567 Msa0466070:CDS 55.0%
GGCTTCAAGGTTGAGAGACC+AGG + chr3_3:66629199-66629218 Msa0466070:CDS 55.0%
CAGGTGTGCATGCACGCATT+CGG + chr3_3:66629548-66629567 Msa0466070:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 66629148 66630038 66629148 ID=Msa0466070;Name=Msa0466070
chr3_3 mRNA 66629148 66630038 66629148 ID=Msa0466070-mRNA-1;Parent=Msa0466070;Name=Msa0466070-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0|0|1|1|1|4|0|144
chr3_3 exon 66629148 66629240 66629148 ID=Msa0466070-mRNA-1:exon:15138;Parent=Msa0466070-mRNA-1
chr3_3 exon 66629317 66629377 66629317 ID=Msa0466070-mRNA-1:exon:15139;Parent=Msa0466070-mRNA-1
chr3_3 exon 66629545 66629691 66629545 ID=Msa0466070-mRNA-1:exon:15140;Parent=Msa0466070-mRNA-1
chr3_3 exon 66629905 66630038 66629905 ID=Msa0466070-mRNA-1:exon:15141;Parent=Msa0466070-mRNA-1
chr3_3 CDS 66629148 66629240 66629148 ID=Msa0466070-mRNA-1:cds;Parent=Msa0466070-mRNA-1
chr3_3 CDS 66629317 66629377 66629317 ID=Msa0466070-mRNA-1:cds;Parent=Msa0466070-mRNA-1
chr3_3 CDS 66629545 66629691 66629545 ID=Msa0466070-mRNA-1:cds;Parent=Msa0466070-mRNA-1
chr3_3 CDS 66629905 66630038 66629905 ID=Msa0466070-mRNA-1:cds;Parent=Msa0466070-mRNA-1
Gene Sequence

>Msa0466070

TTGGAAACAAAACCAATCATTTTGATAGGAGATGGTGATTCAAGGCATATAGGCTTCAAGGTTGAGAGACCAGGTGCTTATGAAATTACTTCTAATGAAGTCACTGTAGGACGTGTTCCAGAGAAAGCTGATTTAGTGATCCCAGTTGCAACAGTGTCAGGTGTGCATGCACGCATTCGGATGAAACAAGACAATCTTCTTGTTATAGATTTGGATAGCACCAATGGAACATTCATTGGTGACAAAAGGCTGAAACCTGGAGTAGTTACCACTGTATCTTCTGGGAGTTATATTACTTTTGGGGACACTAATTTGGCTATGTTCCGTGTGTCGAAAATAGAAGAGAAGGCTGCAGATACAGTTGGAGAACCAGAAGGTGAACTAGACAATGGTGACAAATCTGATAGTACTGAAACAAGTTCAACTTCTAGTTGA

Protein sequence

>Msa0466070

LETKPIILIGDGDSRHIGFKVERPGAYEITSNEVTVGRVPEKADLVIPVATVSGVHARIRMKQDNLLVIDLDSTNGTFIGDKRLKPGVVTTVSSGSYITFGDTNLAMFRVSKIEEKAADTVGEPEGELDNGDKSDSTETSSTSS*