AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0936110


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0936110 MtrunA17_Chr6g0451941 96.689 151 5 0 1 151 1 151 2.13e-108 305
Msa0936110 MtrunA17_Chr7g0262351 33.628 113 74 1 25 137 14 125 1.94e-17 73.9
Msa0936110 MtrunA17_Chr8g0364781 34.259 108 69 1 33 138 12 119 4.50e-15 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0936110 AT5G26594.1 31.250 112 77 0 33 144 18 129 3.72e-17 73.6

Find 29 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTCTCGGGTCAAAGGTTT+TGG 0.171590 6_3:-6738799 None:intergenic
TACCTCGGGTCCATTGATTA+TGG 0.250485 6_3:-6738128 None:intergenic
AGCAATGCATTCATTGGATA+TGG 0.328332 6_3:-6737953 None:intergenic
CATCATATGCTTGAATCAAT+AGG 0.390164 6_3:+6738010 Msa0936110:CDS
TTTGATTTGCCCATAATCAA+TGG 0.409566 6_3:+6738118 Msa0936110:CDS
GATCAAAATGTGCAAATGTT+TGG 0.412226 6_3:+6738751 Msa0936110:CDS
CACTATGTGCAGGCTCTGTT+CGG 0.424190 6_3:-6738036 None:intergenic
ACCTCGGGTCCATTGATTAT+GGG 0.437317 6_3:-6738127 None:intergenic
TCTACTAGCAATGCATTCAT+TGG 0.442738 6_3:-6737959 None:intergenic
GTGAGGCAGATGCGTGCAAT+GGG 0.459873 6_3:+6738688 Msa0936110:CDS
CATATGATGCTCTAAGCGTC+TGG 0.510351 6_3:-6737996 None:intergenic
TGATGAACACAAAACTCTCT+CGG 0.519844 6_3:-6738813 None:intergenic
ACAAAACTCTCTCGGGTCAA+AGG 0.520328 6_3:-6738805 None:intergenic
ATGAATGCATTGCTAGTAGA+TGG 0.520529 6_3:+6737962 Msa0936110:CDS
GATGAACACAAAACTCTCTC+GGG 0.532140 6_3:-6738812 None:intergenic
GGGATACAGACCAAGGTGGT+TGG 0.534297 6_3:+6738709 Msa0936110:CDS
GCTTCTTGAGCACTATGTGC+AGG 0.556886 6_3:-6738046 None:intergenic
AAGTTGCAATCAACAATGGA+TGG 0.566106 6_3:+6737851 None:intergenic
GGTGAGGCAGATGCGTGCAA+TGG 0.598157 6_3:+6738687 Msa0936110:CDS
TGTTAACATTCCAACCACCT+TGG 0.598528 6_3:-6738719 None:intergenic
AACAATGGATGGAGGAACCA+CGG 0.600766 6_3:+6737862 None:intergenic
ATCTGCATTAGTTTCACATG+CGG 0.612322 6_3:-6738849 None:intergenic
ACAATGGATGGAGGAACCAC+GGG 0.635016 6_3:+6737863 None:intergenic
GCCCATAATCAATGGACCCG+AGG 0.655096 6_3:+6738126 Msa0936110:CDS
GAGGAACCACGGGATATAAG+CGG 0.658571 6_3:+6737873 Msa0936110:CDS
TTGCAATCAACAATGGATGG+AGG 0.668830 6_3:+6737854 None:intergenic
TGCAATGGGGATACAGACCA+AGG 0.690928 6_3:+6738702 Msa0936110:CDS
TGAGGCAGATGCGTGCAATG+GGG 0.781176 6_3:+6738689 Msa0936110:CDS
AATGGGGATACAGACCAAGG+TGG 0.794219 6_3:+6738705 Msa0936110:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATAAATTTTTGATACCT+CGG - chr6_3:6738146-6738165 None:intergenic 15.0%
!!! TAAATAAATTTTTGATACCT+CGG - chr6_3:6738146-6738165 None:intergenic 15.0%
!!! AAATAAATTTTTGATACCTC+GGG - chr6_3:6738145-6738164 None:intergenic 20.0%
!!! AAACTAGTTAGTTTAAAATG+TGG - chr6_3:6738202-6738221 None:intergenic 20.0%
!! AAGTTAATCTCATATTTAGA+CGG + chr6_3:6738248-6738267 Msa0936110:intron 20.0%
!! TTAAATTGACAACTCATTTA+TGG - chr6_3:6738597-6738616 None:intergenic 20.0%
!!! AAATAAATTTTTGATACCTC+GGG - chr6_3:6738145-6738164 None:intergenic 20.0%
!!! AAACTAGTTAGTTTAAAATG+TGG - chr6_3:6738202-6738221 None:intergenic 20.0%
!! AAGTTAATCTCATATTTAGA+CGG + chr6_3:6738248-6738267 Msa0936110:intron 20.0%
!! TTAAATTGACAACTCATTTA+TGG - chr6_3:6738597-6738616 None:intergenic 20.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6_3:6738435-6738454 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6_3:6738666-6738685 Msa0936110:intron 25.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6_3:6738435-6738454 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6_3:6738666-6738685 Msa0936110:intron 25.0%
CATCATATGCTTGAATCAAT+AGG + chr6_3:6738010-6738029 Msa0936110:CDS 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6_3:6738118-6738137 Msa0936110:CDS 30.0%
TTAATCTCATATTTAGACGG+TGG + chr6_3:6738251-6738270 Msa0936110:intron 30.0%
TAATCTCATATTTAGACGGT+GGG + chr6_3:6738252-6738271 Msa0936110:intron 30.0%
TGAGATGAATTCTTATCAAC+TGG + chr6_3:6738378-6738397 Msa0936110:intron 30.0%
!!! TCAACTGGACTATTTTTTGT+TGG + chr6_3:6738393-6738412 Msa0936110:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6_3:6738451-6738470 Msa0936110:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6_3:6738456-6738475 None:intergenic 30.0%
ATTTATGGACTTGGATTTGA+CGG - chr6_3:6738582-6738601 None:intergenic 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6_3:6738671-6738690 None:intergenic 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6_3:6738671-6738690 Msa0936110:intron 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6_3:6738751-6738770 Msa0936110:CDS 30.0%
CATCATATGCTTGAATCAAT+AGG + chr6_3:6738010-6738029 Msa0936110:CDS 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6_3:6738118-6738137 Msa0936110:CDS 30.0%
TTAATCTCATATTTAGACGG+TGG + chr6_3:6738251-6738270 Msa0936110:intron 30.0%
TAATCTCATATTTAGACGGT+GGG + chr6_3:6738252-6738271 Msa0936110:intron 30.0%
TGAGATGAATTCTTATCAAC+TGG + chr6_3:6738378-6738397 Msa0936110:intron 30.0%
!!! TCAACTGGACTATTTTTTGT+TGG + chr6_3:6738393-6738412 Msa0936110:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6_3:6738451-6738470 Msa0936110:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6_3:6738456-6738475 None:intergenic 30.0%
ATTTATGGACTTGGATTTGA+CGG - chr6_3:6738582-6738601 None:intergenic 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6_3:6738671-6738690 None:intergenic 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6_3:6738671-6738690 Msa0936110:intron 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6_3:6738751-6738770 Msa0936110:CDS 30.0%
!!! ATCCACATTTTTTTCTCCTC+TGG - chr6_3:6737908-6737927 None:intergenic 35.0%
AGCAATGCATTCATTGGATA+TGG - chr6_3:6737956-6737975 None:intergenic 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6_3:6737962-6737981 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6_3:6737962-6737981 Msa0936110:CDS 35.0%
TCTCACGTATTTCTTTGTTC+TGG - chr6_3:6738290-6738309 None:intergenic 35.0%
TGAGACTCATATTTAGACAC+TGG + chr6_3:6738305-6738324 Msa0936110:intron 35.0%
TATCTCATAGCTGAACTATC+TGG - chr6_3:6738488-6738507 None:intergenic 35.0%
AATCAAACAACCTCACTTGA+TGG + chr6_3:6738526-6738545 Msa0936110:intron 35.0%
TGACAACTCATTTATGGACT+TGG - chr6_3:6738591-6738610 None:intergenic 35.0%
TGATGAACACAAAACTCTCT+CGG - chr6_3:6738816-6738835 None:intergenic 35.0%
!! AGAGTTTTGTGTTCATCACT+GGG + chr6_3:6738818-6738837 Msa0936110:CDS 35.0%
!!! ATCCACATTTTTTTCTCCTC+TGG - chr6_3:6737908-6737927 None:intergenic 35.0%
AGCAATGCATTCATTGGATA+TGG - chr6_3:6737956-6737975 None:intergenic 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6_3:6737962-6737981 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6_3:6737962-6737981 Msa0936110:CDS 35.0%
TCTCACGTATTTCTTTGTTC+TGG - chr6_3:6738290-6738309 None:intergenic 35.0%
TGAGACTCATATTTAGACAC+TGG + chr6_3:6738305-6738324 Msa0936110:intron 35.0%
TATCTCATAGCTGAACTATC+TGG - chr6_3:6738488-6738507 None:intergenic 35.0%
AATCAAACAACCTCACTTGA+TGG + chr6_3:6738526-6738545 Msa0936110:intron 35.0%
TGACAACTCATTTATGGACT+TGG - chr6_3:6738591-6738610 None:intergenic 35.0%
TGATGAACACAAAACTCTCT+CGG - chr6_3:6738816-6738835 None:intergenic 35.0%
!! AGAGTTTTGTGTTCATCACT+GGG + chr6_3:6738818-6738837 Msa0936110:CDS 35.0%
AGCCAGAGGAGAAAAAAATG+TGG + chr6_3:6737903-6737922 Msa0936110:CDS 40.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6_3:6738067-6738086 Msa0936110:CDS 40.0%
ATATTTAGACGGTGGGTCTT+TGG + chr6_3:6738259-6738278 Msa0936110:intron 40.0%
TATTTAGACGGTGGGTCTTT+GGG + chr6_3:6738260-6738279 Msa0936110:intron 40.0%
GACTCATATTTAGACACTGG+CGG + chr6_3:6738308-6738327 Msa0936110:intron 40.0%
TGTTAACATTCCAACCACCT+TGG - chr6_3:6738722-6738741 None:intergenic 40.0%
GATGAACACAAAACTCTCTC+GGG - chr6_3:6738815-6738834 None:intergenic 40.0%
!! GAGAGTTTTGTGTTCATCAC+TGG + chr6_3:6738817-6738836 Msa0936110:CDS 40.0%
AGCCAGAGGAGAAAAAAATG+TGG + chr6_3:6737903-6737922 Msa0936110:CDS 40.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6_3:6738067-6738086 Msa0936110:CDS 40.0%
ATATTTAGACGGTGGGTCTT+TGG + chr6_3:6738259-6738278 Msa0936110:intron 40.0%
TATTTAGACGGTGGGTCTTT+GGG + chr6_3:6738260-6738279 Msa0936110:intron 40.0%
GACTCATATTTAGACACTGG+CGG + chr6_3:6738308-6738327 Msa0936110:intron 40.0%
TGTTAACATTCCAACCACCT+TGG - chr6_3:6738722-6738741 None:intergenic 40.0%
GATGAACACAAAACTCTCTC+GGG - chr6_3:6738815-6738834 None:intergenic 40.0%
!! GAGAGTTTTGTGTTCATCAC+TGG + chr6_3:6738817-6738836 Msa0936110:CDS 40.0%
!! TTTTTGCCGCTTATATCCCG+TGG - chr6_3:6737882-6737901 None:intergenic 45.0%
TAAGCGGCAAAAAAAGCCAG+AGG + chr6_3:6737889-6737908 Msa0936110:CDS 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6_3:6737999-6738018 None:intergenic 45.0%
! ACCTCGGGTCCATTGATTAT+GGG - chr6_3:6738130-6738149 None:intergenic 45.0%
! TACCTCGGGTCCATTGATTA+TGG - chr6_3:6738131-6738150 None:intergenic 45.0%
GGTATCCTCATACTGACGAT+GGG + chr6_3:6738329-6738348 Msa0936110:intron 45.0%
TGAAACCCATCGTCAGTATG+AGG - chr6_3:6738337-6738356 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+AGG - chr6_3:6738539-6738558 None:intergenic 45.0%
! TCTCTCGGGTCAAAGGTTTT+GGG - chr6_3:6738801-6738820 None:intergenic 45.0%
ACAAAACTCTCTCGGGTCAA+AGG - chr6_3:6738808-6738827 None:intergenic 45.0%
!! TTTTTGCCGCTTATATCCCG+TGG - chr6_3:6737882-6737901 None:intergenic 45.0%
TAAGCGGCAAAAAAAGCCAG+AGG + chr6_3:6737889-6737908 Msa0936110:CDS 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6_3:6737999-6738018 None:intergenic 45.0%
! ACCTCGGGTCCATTGATTAT+GGG - chr6_3:6738130-6738149 None:intergenic 45.0%
! TACCTCGGGTCCATTGATTA+TGG - chr6_3:6738131-6738150 None:intergenic 45.0%
GGTATCCTCATACTGACGAT+GGG + chr6_3:6738329-6738348 Msa0936110:intron 45.0%
TGAAACCCATCGTCAGTATG+AGG - chr6_3:6738337-6738356 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+AGG - chr6_3:6738539-6738558 None:intergenic 45.0%
! TCTCTCGGGTCAAAGGTTTT+GGG - chr6_3:6738801-6738820 None:intergenic 45.0%
ACAAAACTCTCTCGGGTCAA+AGG - chr6_3:6738808-6738827 None:intergenic 45.0%
GAGGAACCACGGGATATAAG+CGG + chr6_3:6737873-6737892 Msa0936110:CDS 50.0%
CACTATGTGCAGGCTCTGTT+CGG - chr6_3:6738039-6738058 None:intergenic 50.0%
GCTTCTTGAGCACTATGTGC+AGG - chr6_3:6738049-6738068 None:intergenic 50.0%
CGGTATCCTCATACTGACGA+TGG + chr6_3:6738328-6738347 Msa0936110:intron 50.0%
TGCAATGGGGATACAGACCA+AGG + chr6_3:6738702-6738721 Msa0936110:CDS 50.0%
AATGGGGATACAGACCAAGG+TGG + chr6_3:6738705-6738724 Msa0936110:CDS 50.0%
! CTCTCGGGTCAAAGGTTTTG+GGG - chr6_3:6738800-6738819 None:intergenic 50.0%
! CTCTCTCGGGTCAAAGGTTT+TGG - chr6_3:6738802-6738821 None:intergenic 50.0%
GAGGAACCACGGGATATAAG+CGG + chr6_3:6737873-6737892 Msa0936110:CDS 50.0%
CACTATGTGCAGGCTCTGTT+CGG - chr6_3:6738039-6738058 None:intergenic 50.0%
GCTTCTTGAGCACTATGTGC+AGG - chr6_3:6738049-6738068 None:intergenic 50.0%
CGGTATCCTCATACTGACGA+TGG + chr6_3:6738328-6738347 Msa0936110:intron 50.0%
TGCAATGGGGATACAGACCA+AGG + chr6_3:6738702-6738721 Msa0936110:CDS 50.0%
AATGGGGATACAGACCAAGG+TGG + chr6_3:6738705-6738724 Msa0936110:CDS 50.0%
! CTCTCGGGTCAAAGGTTTTG+GGG - chr6_3:6738800-6738819 None:intergenic 50.0%
! CTCTCTCGGGTCAAAGGTTT+TGG - chr6_3:6738802-6738821 None:intergenic 50.0%
GCCCATAATCAATGGACCCG+AGG + chr6_3:6738126-6738145 Msa0936110:CDS 55.0%
GTGAGGCAGATGCGTGCAAT+GGG + chr6_3:6738688-6738707 Msa0936110:CDS 55.0%
TGAGGCAGATGCGTGCAATG+GGG + chr6_3:6738689-6738708 Msa0936110:CDS 55.0%
GGGATACAGACCAAGGTGGT+TGG + chr6_3:6738709-6738728 Msa0936110:CDS 55.0%
!!! GGTCAAAGGTTTTGGGGTGC+TGG - chr6_3:6738794-6738813 None:intergenic 55.0%
GCCCATAATCAATGGACCCG+AGG + chr6_3:6738126-6738145 Msa0936110:CDS 55.0%
GTGAGGCAGATGCGTGCAAT+GGG + chr6_3:6738688-6738707 Msa0936110:CDS 55.0%
TGAGGCAGATGCGTGCAATG+GGG + chr6_3:6738689-6738708 Msa0936110:CDS 55.0%
GGGATACAGACCAAGGTGGT+TGG + chr6_3:6738709-6738728 Msa0936110:CDS 55.0%
!!! GGTCAAAGGTTTTGGGGTGC+TGG - chr6_3:6738794-6738813 None:intergenic 55.0%
GGTGAGGCAGATGCGTGCAA+TGG + chr6_3:6738687-6738706 Msa0936110:CDS 60.0%
GGTGAGGCAGATGCGTGCAA+TGG + chr6_3:6738687-6738706 Msa0936110:CDS 60.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 6737866 6738858 6737866 ID=Msa0936110;Name=Msa0936110
chr6_3 mRNA 6737866 6738858 6737866 ID=Msa0936110-mRNA-1;Parent=Msa0936110;Name=Msa0936110-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|151
chr6_3 exon 6737866 6738147 6737866 ID=Msa0936110-mRNA-1:exon:2135;Parent=Msa0936110-mRNA-1
chr6_3 exon 6738685 6738858 6738685 ID=Msa0936110-mRNA-1:exon:2136;Parent=Msa0936110-mRNA-1
chr6_3 CDS 6737866 6738147 6737866 ID=Msa0936110-mRNA-1:cds;Parent=Msa0936110-mRNA-1
chr6_3 CDS 6738685 6738858 6738685 ID=Msa0936110-mRNA-1:cds;Parent=Msa0936110-mRNA-1
Gene Sequence

>Msa0936110

ATGGATGGAGGAACCACGGGATATAAGCGGCAAAAAAAGCCAGAGGAGAAAAAAATGTGGATCAAAAATCGTGAATTATATGACACTCCATATCCAATGAATGCATTGCTAGTAGATGGTGTGACTGCAACCAGACGCTTAGAGCATCATATGCTTGAATCAATAGGCATCCGAACAGAGCCTGCACATAGTGCTCAAGAAGCGATGCAAATTTTGTTGACTGGTGTCAAATTTGACTTCATATTTGTTGATTTTGATTTGCCCATAATCAATGGACCCGAGTTGGTGAGGCAGATGCGTGCAATGGGGATACAGACCAAGGTGGTTGGAATGTTAACAAACTTCAATGATCAAAATGTGCAAATGTTTGGAGAAGCAAGAGCTAATGCCAGCACCCCAAAACCTTTGACCCGAGAGAGTTTTGTGTTCATCACTGGGATCTTGCGCCGCATGTGA

Protein sequence

>Msa0936110

MDGGTTGYKRQKKPEEKKMWIKNRELYDTPYPMNALLVDGVTATRRLEHHMLESIGIRTEPAHSAQEAMQILLTGVKFDFIFVDFDLPIINGPELVRQMRAMGIQTKVVGMLTNFNDQNVQMFGEARANASTPKPLTRESFVFITGILRRM*