AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG025858

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025858 MtrunA17_Chr5g0406791 92.593 162 12 0 1 162 1 162 3.53e-110 314
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG025858 AT4G35700.1 32.609 184 103 8 76 246 98 273 3.06e-17 79.3
MsaG025858 AT4G35610.1 54.000 50 23 0 107 156 129 178 2.10e-13 68.6

Find 96 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGTTTCATCATCCTCTTC+TGG 0.204274 5:-13555013 None:intergenic
GTGGCTGGTGTGGTGTTGTT+TGG 0.232681 5:-13553631 None:intergenic
GCATCCAGAGCGTGCTCATC+GGG 0.273262 5:+13554011 MsaT025858.1:CDS
GAAAACTCCCTCTTGCATTC+TGG 0.285785 5:-13553955 None:intergenic
CAGATGAACCGTCGGCAGTT+AGG 0.305066 5:-13553843 None:intergenic
TCTTGCATTCTGGACATGTT+GGG 0.316539 5:-13553945 None:intergenic
TGGCTGGTGTGGTGTTGTTT+GGG 0.349412 5:-13553630 None:intergenic
TCCACATGGAAAGCTGCGTT+TGG 0.354309 5:+13553976 MsaT025858.1:CDS
TTCGCAGCCGGTGCAGGTGC+TGG 0.355655 5:-13554944 None:intergenic
CTCTTGCATTCTGGACATGT+TGG 0.358689 5:-13553946 None:intergenic
GTGCAGGTGCAGGTGCTGCT+TGG 0.361541 5:-13554922 None:intergenic
GTTGTTTGGGCTTGACTCAT+TGG 0.370557 5:-13553617 None:intergenic
GCCGGTGCAGGTGCTGGTGC+AGG 0.376765 5:-13554938 None:intergenic
AGATGAACCGTCGGCAGTTA+GGG 0.382592 5:-13553842 None:intergenic
TACCCTCATCACCACCATTT+GGG 0.382708 5:-13553780 None:intergenic
CAGAGGACCCTGCGGTTGAT+TGG 0.396020 5:-13554868 None:intergenic
CTGATGGAGGGTCTTTCACT+TGG 0.398758 5:-13553918 None:intergenic
CCACATGGAAAGCTGCGTTT+GGG 0.406183 5:+13553977 MsaT025858.1:CDS
GCAGGTGCTGGTGCAGGTGC+AGG 0.406183 5:-13554932 None:intergenic
TCTTCATTCGCAGCCGGTGC+AGG 0.409609 5:-13554950 None:intergenic
TTACCCTCATCACCACCATT+TGG 0.414014 5:-13553781 None:intergenic
TTTGGGCTTGACTCATTGGC+AGG 0.414848 5:-13553613 None:intergenic
GGGTCCTCTGCTGGTGGTAG+TGG 0.416926 5:+13554881 MsaT025858.1:CDS
ATCATCATCGTCAGTTAGTT+CGG 0.423637 5:-13553749 None:intergenic
GACCATCAGAACCAACTTGT+TGG 0.435442 5:-13553870 None:intergenic
TCCTCAGTGTTTGTCACAGC+GGG 0.444401 5:-13553691 None:intergenic
TCATCATCCTCTTCTGGAGG+TGG 0.459723 5:-13555007 None:intergenic
ATGGTCAAGTCTTCAAGAAA+AGG 0.463536 5:+13553887 MsaT025858.1:CDS
GTTCAGCCAAGGTGCGTTGA+GGG 0.469269 5:-13553657 None:intergenic
TTGTTTACAGGTGATGGTCT+TGG 0.469520 5:+13554779 MsaT025858.1:intron
ATCCAACAAGTTGGTTCTGA+TGG 0.472826 5:+13553868 MsaT025858.1:CDS
GAAAACACCGGAGGAAGTCC+TGG 0.473695 5:+13553726 MsaT025858.1:CDS
CAAGGTGCGTTGAGGGGAAG+TGG 0.482830 5:-13553650 None:intergenic
TCAACCGCAGGGTCCTCTGC+TGG 0.483755 5:+13554872 MsaT025858.1:CDS
CACTTCCCCTCAACGCACCT+TGG 0.498843 5:+13553651 MsaT025858.1:CDS
CATGTTGGGGATCCTGATGG+AGG 0.503638 5:-13553931 None:intergenic
GGACATGTTGGGGATCCTGA+TGG 0.504468 5:-13553934 None:intergenic
CTTGCATTCTGGACATGTTG+GGG 0.506162 5:-13553944 None:intergenic
ATATATACCCTCAGCAGGAA+TGG 0.511286 5:-13554070 None:intergenic
CAAGTGAAAGACCCTCCATC+AGG 0.513855 5:+13553919 MsaT025858.1:CDS
GTGCGTTGAGGGGAAGTGGC+TGG 0.516360 5:-13553646 None:intergenic
CTTGGCGACAAGATCAATGA+AGG 0.517419 5:+13554797 MsaT025858.1:CDS
AGCATCCAGAGCGTGCTCAT+CGG 0.517955 5:+13554010 MsaT025858.1:CDS
TATATACCCTCAGCAGGAAT+GGG 0.519334 5:-13554069 None:intergenic
GTCATATATATACCCTCAGC+AGG 0.521947 5:-13554075 None:intergenic
GAATGAAGAAAGACCGAGAC+GGG 0.526992 5:+13554964 MsaT025858.1:CDS
GATGATGATTTGATCCCAAA+TGG 0.535324 5:+13553766 MsaT025858.1:CDS
TCATCTGTTATCCAACAAGT+TGG 0.537358 5:+13553859 MsaT025858.1:CDS
GTTTCATCATCCTCTTCTGG+AGG 0.539642 5:-13555010 None:intergenic
GGTCTTTCTTCATTCGCAGC+CGG 0.542101 5:-13554956 None:intergenic
ATGTTGGGGATCCTGATGGA+GGG 0.546248 5:-13553930 None:intergenic
AGTTCGGCCAGGACTTCCTC+CGG 0.548973 5:-13553733 None:intergenic
CGTTGCACCCATTCCTGCTG+AGG 0.553957 5:+13554062 MsaT025858.1:CDS
CATCGTCAGTTAGTTCGGCC+AGG 0.555694 5:-13553744 None:intergenic
ACCTGCACCAGCACCTGCAC+CGG 0.556575 5:+13554937 MsaT025858.1:CDS
TTGAGGGGAAGTGGCTGGTG+TGG 0.560312 5:-13553641 None:intergenic
TTCAGATCAAAGTCCCGTCT+CGG 0.562388 5:-13554977 None:intergenic
AGATCGATCCAATCAACCGC+AGG 0.563542 5:+13554860 MsaT025858.1:CDS
CGAGTTGCCACCTCCAGAAG+AGG 0.565350 5:+13555000 MsaT025858.1:CDS
AGGGTAACGAAGAAGACGAT+GGG 0.573776 5:+13553797 MsaT025858.1:CDS
CAAGTCTTCAAGAAAAGGAA+AGG 0.585799 5:+13553892 MsaT025858.1:CDS
TCAGTGTTTGTCACAGCGGG+TGG 0.591498 5:-13553688 None:intergenic
GCAACGGTGCTAAAAGTTGG+TGG 0.591524 5:-13554045 None:intergenic
ACCGCAGGGTCCTCTGCTGG+TGG 0.592667 5:+13554875 MsaT025858.1:CDS
CTCAGCAGGAATGGGTGCAA+CGG 0.592995 5:-13554061 None:intergenic
ATCCAGAGCGTGCTCATCGG+GGG 0.598304 5:+13554013 MsaT025858.1:CDS
ACGGTGCTAAAAGTTGGTGG+AGG 0.599469 5:-13554042 None:intergenic
TTCAGCCAAGGTGCGTTGAG+GGG 0.602294 5:-13553656 None:intergenic
TTGGGCTTGACTCATTGGCA+GGG 0.602976 5:-13553612 None:intergenic
TGTTCAGCCAAGGTGCGTTG+AGG 0.606127 5:-13553658 None:intergenic
ATCCCAAATGGTGGTGATGA+GGG 0.607792 5:+13553778 MsaT025858.1:CDS
CAACATGTCCAGAATGCAAG+AGG 0.611183 5:+13553947 MsaT025858.1:CDS
TGGCTGATCATGTTCAGCCA+AGG 0.612094 5:-13553668 None:intergenic
TGGTAGTGGTCATATCACTA+AGG 0.615054 5:+13554895 MsaT025858.1:CDS
TGAAACCTCTCTGAAAACAC+CGG 0.622863 5:+13553714 MsaT025858.1:CDS
TTGGCGACAAGATCAATGAA+GGG 0.623712 5:+13554798 MsaT025858.1:CDS
GTTGCACCCATTCCTGCTGA+GGG 0.624536 5:+13554063 MsaT025858.1:CDS
GATCCCAAATGGTGGTGATG+AGG 0.627502 5:+13553777 MsaT025858.1:CDS
ATCCTCAGTGTTTGTCACAG+CGG 0.628423 5:-13553692 None:intergenic
GGTGCAACGGTGCTAAAAGT+TGG 0.632688 5:-13554048 None:intergenic
CGGTGCTAAAAGTTGGTGGA+GGG 0.635586 5:-13554041 None:intergenic
GAGGGTAACGAAGAAGACGA+TGG 0.641669 5:+13553796 MsaT025858.1:CDS
ATGACCACTACCACCAGCAG+AGG 0.645607 5:-13554885 None:intergenic
TTGGATAACAGATGAACCGT+CGG 0.650442 5:-13553851 None:intergenic
CATCCAGAGCGTGCTCATCG+GGG 0.656726 5:+13554012 MsaT025858.1:CDS
GATCGATCCAATCAACCGCA+GGG 0.660372 5:+13554861 MsaT025858.1:CDS
CCCAAACGCAGCTTTCCATG+TGG 0.665261 5:-13553977 None:intergenic
TGGCGACAAGATCAATGAAG+GGG 0.669025 5:+13554799 MsaT025858.1:CDS
GTTATCGCCCTAACTGCCGA+CGG 0.669691 5:+13553835 MsaT025858.1:CDS
AACATGTCCAGAATGCAAGA+GGG 0.691308 5:+13553948 MsaT025858.1:CDS
AACCTCTCTGAAAACACCGG+AGG 0.709220 5:+13553717 MsaT025858.1:CDS
ACCACCAGCAGAGGACCCTG+CGG 0.721168 5:-13554876 None:intergenic
CGAATGAAGAAAGACCGAGA+CGG 0.721426 5:+13554963 MsaT025858.1:CDS
GGGTAACGAAGAAGACGATG+GGG 0.737196 5:+13553798 MsaT025858.1:CDS
GATGATTTGATCCCAAATGG+TGG 0.741325 5:+13553769 MsaT025858.1:CDS
ACCCGCTGTGACAAACACTG+AGG 0.799006 5:+13553690 MsaT025858.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr5 gene 13553601 13555045 13553601 ID=MsaG025858
Chr5 mRNA 13553601 13555045 13553601 ID=MsaT025858.1;Parent=MsaG025858
Chr5 exon 13553601 13554084 13553601 ID=MsaT025858.1.exon1;Parent=MsaT025858.1
Chr5 CDS 13553601 13554084 13553601 ID=cds.MsaT025858.1;Parent=MsaT025858.1
Chr5 exon 13554789 13555045 13554789 ID=MsaT025858.1.exon2;Parent=MsaT025858.1
Chr5 CDS 13554789 13555045 13554789 ID=cds.MsaT025858.1;Parent=MsaT025858.1
Gene Sequence

>MsaT025858.1

ATGGAAAACGTCCCTGCCAATGAGTCAAGCCCAAACAACACCACACCAGCCACTTCCCCTCAACGCACCTTGGCTGAACATGATCAGCCACCCGCTGTGACAAACACTGAGGATGAAACCTCTCTGAAAACACCGGAGGAAGTCCTGGCCGAACTAACTGACGATGATGATGATTTGATCCCAAATGGTGGTGATGAGGGTAACGAAGAAGACGATGGGGCTTTTAGGACGATGGTTATCGCCCTAACTGCCGACGGTTCATCTGTTATCCAACAAGTTGGTTCTGATGGTCAAGTCTTCAAGAAAAGGAAAGGCAACCAAGTGAAAGACCCTCCATCAGGATCCCCAACATGTCCAGAATGCAAGAGGGAGTTTTCCACATGGAAAGCTGCGTTTGGGCATATGCGCAAGCATCCAGAGCGTGCTCATCGGGGGTTTTTCCCTCCACCAACTTTTAGCACCGTTGCACCCATTCCTGCTGAGGGTGATGGTCTTGGCGACAAGATCAATGAAGGGGTGAGCTCATTAGCTCGCGAGCTTGTGTTCGATCTGAATAGATCGATCCAATCAACCGCAGGGTCCTCTGCTGGTGGTAGTGGTCATATCACTAAGGAAATCCAAGCAGCACCTGCACCTGCACCAGCACCTGCACCGGCTGCGAATGAAGAAAGACCGAGACGGGACTTTGATCTGAACGAGTTGCCACCTCCAGAAGAGGATGATGAAACAGAAGAGAAATGA
Protein sequence

>MsaT025858.1

MENVPANESSPNNTTPATSPQRTLAEHDQPPAVTNTEDETSLKTPEEVLAELTDDDDDLIPNGGDEGNEEDDGAFRTMVIALTADGSSVIQQVGSDGQVFKKRKGNQVKDPPSGSPTCPECKREFSTWKAAFGHMRKHPERAHRGFFPPPTFSTVAPIPAEGDGLGDKINEGVSSLARELVFDLNRSIQSTAGSSAGGSGHITKEIQAAPAPAPAPAPAANEERPRRDFDLNELPPPEEDDETEEK*