AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0436460


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTGTCGTTGTCGGCTATT+TGG 0.216325 3_2:+90040020 None:intergenic
GGCGGGGAACCCATGAAATT+TGG 0.274459 3_2:-90039979 Msa0436460:CDS
CGCTCTCCACACCGTCCATT+GGG 0.361017 3_2:+90039765 None:intergenic
ACCGAGCACGCCAAATTTCA+TGG 0.361507 3_2:+90039969 None:intergenic
GTTGTCGTTGTCGGCTATTT+GGG 0.377596 3_2:+90040021 None:intergenic
GTTGTCGGCTATTTGGGTTT+TGG 0.377940 3_2:+90040027 None:intergenic
ATGGGTTCCCCGCCAGTGTA+TGG 0.378975 3_2:+90039988 None:intergenic
ACGGTGTGGAGAGCGATTTA+TGG 0.387961 3_2:-90039757 Msa0436460:CDS
TTGCTCAGACCACTGAAGTT+GGG 0.412418 3_2:+90039857 None:intergenic
TGTCTCCGGCGTTGTGAAGA+AGG 0.439983 3_2:+90039891 None:intergenic
CCCATGAAATTTGGCGTGCT+CGG 0.450530 3_2:-90039970 Msa0436460:intron
GGTCATTGTTGACAAGATCT+AGG 0.455636 3_2:-90039808 Msa0436460:CDS
ACGCCGGAGACACGAGATCT+AGG 0.456123 3_2:-90039880 Msa0436460:CDS
TCGCTCTCCACACCGTCCAT+TGG 0.457821 3_2:+90039764 None:intergenic
CGGTGTGGAGAGCGATTTAT+GGG 0.459062 3_2:-90039756 Msa0436460:CDS
GGGCTAATACCACTTGAGTT+GGG 0.464825 3_2:+90039785 None:intergenic
TGGGTCGTCAGTGACGAGAT+TGG 0.479654 3_2:-90039737 Msa0436460:CDS
GGGTCGTCAGTGACGAGATT+GGG 0.488139 3_2:-90039736 Msa0436460:CDS
TGGGCTAATACCACTTGAGT+TGG 0.493264 3_2:+90039784 None:intergenic
ATTATACACCATACACTGGC+GGG 0.503855 3_2:-90039996 Msa0436460:CDS
GTTGCTCAGACCACTGAAGT+TGG 0.509679 3_2:+90039856 None:intergenic
CCTAACGGAATAGTCGTGTC+TGG 0.519833 3_2:-90040063 Msa0436460:intron
AAAACGCTCTCTTCATCAGT+TGG 0.519969 3_2:+90039834 None:intergenic
GTCAGTGACGAGATTGGGTA+AGG 0.523532 3_2:-90039731 None:intergenic
CCGAGCACGCCAAATTTCAT+GGG 0.529791 3_2:+90039970 None:intergenic
GGGCCTAGATCTCGTGTCTC+CGG 0.553368 3_2:+90039877 None:intergenic
GTCTCCGGCGTTGTGAAGAA+GGG 0.555639 3_2:+90039892 None:intergenic
GTATAATGAGTTGTCGTTGT+CGG 0.567321 3_2:+90040012 None:intergenic
TCCTCCCTTCTTCACAACGC+CGG 0.583529 3_2:-90039896 Msa0436460:CDS
CTCAAGTGGTATTAGCCCAA+TGG 0.604300 3_2:-90039780 Msa0436460:CDS
AGATCTAGGCCCAACTTCAG+TGG 0.618428 3_2:-90039866 Msa0436460:CDS
AGATCTAGGCCCAACTCAAG+TGG 0.625323 3_2:-90039794 Msa0436460:CDS
TTATACACCATACACTGGCG+GGG 0.628230 3_2:-90039995 Msa0436460:CDS
CATTATACACCATACACTGG+CGG 0.637045 3_2:-90039997 Msa0436460:CDS
ACTCATTATACACCATACAC+TGG 0.644543 3_2:-90040000 Msa0436460:CDS
TCCGGCGTTGTGAAGAAGGG+AGG 0.654657 3_2:+90039895 None:intergenic
AGTGGTATTAGCCCAATGGA+CGG 0.656425 3_2:-90039776 Msa0436460:CDS
TATTAGCCCAATGGACGGTG+TGG 0.670800 3_2:-90039771 Msa0436460:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAATTTTTAGGTTTTGGTTT+GGG - chr3_2:90039843-90039862 Msa0436460:CDS 25.0%
GTATATTCATGATCTACTCT+CGG - chr3_2:90039741-90039760 Msa0436460:CDS 30.0%
TATATTCATGATCTACTCTC+GGG - chr3_2:90039742-90039761 Msa0436460:CDS 30.0%
!! CGTTTTATTCCATACATTGA+TGG + chr3_2:90039816-90039835 None:intergenic 30.0%
!!! GTTGTCGAATTTTTAGGTTT+TGG - chr3_2:90039837-90039856 Msa0436460:CDS 30.0%
!!! CGAATTTTTAGGTTTTGGTT+TGG - chr3_2:90039842-90039861 Msa0436460:CDS 30.0%
ATTGGATTGCCATCAATGTA+TGG - chr3_2:90039804-90039823 Msa0436460:CDS 35.0%
! AAACGCGTTGTCGAATTTTT+AGG - chr3_2:90039831-90039850 Msa0436460:CDS 35.0%
GTATAATGAGTTGTCGTTGT+CGG + chr3_2:90039957-90039976 None:intergenic 35.0%
ACTCATTATACACCATACAC+TGG - chr3_2:90039966-90039985 Msa0436460:intron 35.0%
!! GAGTAGGGTAGTGGAATATT+TGG + chr3_2:90039774-90039793 None:intergenic 40.0%
CCAATGAAATCTGGAGAGTA+GGG + chr3_2:90039789-90039808 None:intergenic 40.0%
TCCAATGAAATCTGGAGAGT+AGG + chr3_2:90039790-90039809 None:intergenic 40.0%
GATGGCAATCCAATGAAATC+TGG + chr3_2:90039798-90039817 None:intergenic 40.0%
!!! GGCTATTTGGGTTTTGGTTT+GGG + chr3_2:90039936-90039955 None:intergenic 40.0%
CATTATACACCATACACTGG+CGG - chr3_2:90039969-90039988 Msa0436460:intron 40.0%
ATTATACACCATACACTGGC+GGG - chr3_2:90039970-90039989 Msa0436460:intron 40.0%
AAAACGCTCTCTTCATCAGT+TGG + chr3_2:90040135-90040154 None:intergenic 40.0%
GGTCATTGTTGACAAGATCT+AGG - chr3_2:90040158-90040177 Msa0436460:intron 40.0%
AAATCTGGAGAGTAGGGTAG+TGG + chr3_2:90039783-90039802 None:intergenic 45.0%
CCCTACTCTCCAGATTTCAT+TGG - chr3_2:90039786-90039805 Msa0436460:CDS 45.0%
!!! TTAGGTTTTGGTTTGGGTCG+AGG - chr3_2:90039849-90039868 Msa0436460:CDS 45.0%
CGTAACAGAATAGTCGTGTC+TGG + chr3_2:90039876-90039895 None:intergenic 45.0%
!!! CGGCTATTTGGGTTTTGGTT+TGG + chr3_2:90039937-90039956 None:intergenic 45.0%
!! GTTGTCGGCTATTTGGGTTT+TGG + chr3_2:90039942-90039961 None:intergenic 45.0%
! GTTGTCGTTGTCGGCTATTT+GGG + chr3_2:90039948-90039967 None:intergenic 45.0%
! AGTTGTCGTTGTCGGCTATT+TGG + chr3_2:90039949-90039968 None:intergenic 45.0%
TTATACACCATACACTGGCG+GGG - chr3_2:90039971-90039990 Msa0436460:CDS 45.0%
TTGCTCAGACCACTGAAGTT+GGG + chr3_2:90040112-90040131 None:intergenic 45.0%
!!! CTGATGAAGAGAGCGTTTTG+CGG - chr3_2:90040136-90040155 Msa0436460:intron 45.0%
!!! TGATGAAGAGAGCGTTTTGC+GGG - chr3_2:90040137-90040156 Msa0436460:intron 45.0%
GGGCTAATACCACTTGAGTT+GGG + chr3_2:90040184-90040203 None:intergenic 45.0%
TGGGCTAATACCACTTGAGT+TGG + chr3_2:90040185-90040204 None:intergenic 45.0%
CTCAAGTGGTATTAGCCCAA+TGG - chr3_2:90040186-90040205 Msa0436460:intron 45.0%
AGTGGTATTAGCCCAATGGA+CGG - chr3_2:90040190-90040209 Msa0436460:intron 45.0%
CTGTTACGTACTCCGCCTAA+CGG - chr3_2:90039888-90039907 Msa0436460:CDS 50.0%
GACACGACTATTCCGTTAGG+CGG + chr3_2:90039903-90039922 None:intergenic 50.0%
CCAGACACGACTATTCCGTT+AGG + chr3_2:90039906-90039925 None:intergenic 50.0%
CCTAACGGAATAGTCGTGTC+TGG - chr3_2:90039903-90039922 Msa0436460:CDS 50.0%
!!! TTGGGTTTTGGTTTGGGTCG+AGG + chr3_2:90039930-90039949 None:intergenic 50.0%
CCGAGCACGCCAAATTTCAT+GGG + chr3_2:90039999-90040018 None:intergenic 50.0%
CCCATGAAATTTGGCGTGCT+CGG - chr3_2:90039996-90040015 Msa0436460:CDS 50.0%
ACCGAGCACGCCAAATTTCA+TGG + chr3_2:90040000-90040019 None:intergenic 50.0%
AGATCTAGGCCCAACTTCAG+TGG - chr3_2:90040100-90040119 Msa0436460:intron 50.0%
GTTGCTCAGACCACTGAAGT+TGG + chr3_2:90040113-90040132 None:intergenic 50.0%
AGATCTAGGCCCAACTCAAG+TGG - chr3_2:90040172-90040191 Msa0436460:intron 50.0%
TATTAGCCCAATGGACGGTG+TGG - chr3_2:90040195-90040214 Msa0436460:intron 50.0%
ACGGTGTGGAGAGCGATTTA+TGG - chr3_2:90040209-90040228 Msa0436460:intron 50.0%
CGGTGTGGAGAGCGATTTAT+GGG - chr3_2:90040210-90040229 Msa0436460:intron 50.0%
GGCGGGGAACCCATGAAATT+TGG - chr3_2:90039987-90040006 Msa0436460:CDS 55.0%
TCCTCCCTTCTTCACAACGC+CGG - chr3_2:90040070-90040089 Msa0436460:intron 55.0%
GTCTCCGGCGTTGTGAAGAA+GGG + chr3_2:90040077-90040096 None:intergenic 55.0%
TGTCTCCGGCGTTGTGAAGA+AGG + chr3_2:90040078-90040097 None:intergenic 55.0%
TGGGTCGTCAGTGACGAGAT+TGG - chr3_2:90040229-90040248 Msa0436460:intron 55.0%
GGGTCGTCAGTGACGAGATT+GGG - chr3_2:90040230-90040249 Msa0436460:intron 55.0%
ATGGGTTCCCCGCCAGTGTA+TGG + chr3_2:90039981-90040000 None:intergenic 60.0%
TCCGGCGTTGTGAAGAAGGG+AGG + chr3_2:90040074-90040093 None:intergenic 60.0%
ACGCCGGAGACACGAGATCT+AGG - chr3_2:90040086-90040105 Msa0436460:intron 60.0%
GGGCCTAGATCTCGTGTCTC+CGG + chr3_2:90040092-90040111 None:intergenic 60.0%
CGCTCTCCACACCGTCCATT+GGG + chr3_2:90040204-90040223 None:intergenic 60.0%
TCGCTCTCCACACCGTCCAT+TGG + chr3_2:90040205-90040224 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 90039733 90040255 90039733 ID=Msa0436460;Name=Msa0436460
chr3_2 mRNA 90039733 90040255 90039733 ID=Msa0436460-mRNA-1;Parent=Msa0436460;Name=Msa0436460-mRNA-1;_AED=0.37;_eAED=0.57;_QI=0|0|0|0.66|0|0|3|0|107
chr3_2 exon 90040248 90040255 90040248 ID=Msa0436460-mRNA-1:exon:26780;Parent=Msa0436460-mRNA-1
chr3_2 exon 90039971 90040072 90039971 ID=Msa0436460-mRNA-1:exon:26779;Parent=Msa0436460-mRNA-1
chr3_2 exon 90039733 90039946 90039733 ID=Msa0436460-mRNA-1:exon:26778;Parent=Msa0436460-mRNA-1
chr3_2 CDS 90040248 90040255 90040248 ID=Msa0436460-mRNA-1:cds;Parent=Msa0436460-mRNA-1
chr3_2 CDS 90039971 90040072 90039971 ID=Msa0436460-mRNA-1:cds;Parent=Msa0436460-mRNA-1
chr3_2 CDS 90039733 90039946 90039733 ID=Msa0436460-mRNA-1:cds;Parent=Msa0436460-mRNA-1
Gene Sequence

>Msa0436460

ATGGACGCTCGTGTCTGGTCCTCGACCCAAACCAAAACCCAAATAGCCGACAACGACAACTCATTATACACCATACACTGGCGGGGAACCCATGAAATTTGGCGTGCTCGAGTATATCATATATCTACATATTCATCATCCTCCCTTCTTCACAACGCCGGAGACACGAGATCTAGGCCCAACTTCAGTGGTCTGAGCAACCAACTGATGAAGAGAGCGTTTTGCGGGTCATTGTTGACAAGATCTAGGCCCAACTCAAGTGGTATTAGCCCAATGGACGGTGTGGAGAGCGATTTATGGGTCGTCAGTGACGAGATTGGGTAA

Protein sequence

>Msa0436460

MDARVWSSTQTKTQIADNDNSLYTIHWRGTHEIWRARVYHISTYSSSSLLHNAGDTRSRPNFSGLSNQLMKRAFCGSLLTRSRPNSSGISPMDGVESDLWVVSDEIG*