AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0447810


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0447810 MtrunA17_Chr3g0089161 86.667 105 12 1 1 105 1 103 1.68e-49 155
Msa0447810 MtrunA17_Chr3g0089161 83.871 93 14 1 16 107 95 187 3.62e-46 147
Msa0447810 MtrunA17_Chr4g0019291 72.222 108 27 3 1 106 1 107 2.04e-44 139
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0447810 AT1G51400.1 60.000 110 37 4 1 107 1 106 2.35e-31 107
Msa0447810 AT3G21055.1 54.630 108 41 4 1 106 1 102 5.05e-24 88.6
Msa0447810 AT3G21055.2 54.630 108 41 4 1 106 41 142 1.21e-23 88.6

Find 27 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGCTGTTTGCTCTGTTGC+TGG 0.185357 3_3:-26619790 Msa0447810:CDS
CTGCTGTTTGCTCTGTTGCT+GGG 0.300217 3_3:-26619789 Msa0447810:CDS
ATCCTCAATCCTCGGCTTCC+CGG 0.362856 3_3:-26619965 Msa0447810:CDS
CTCTGTTGCTGGGGTTGCAA+TGG 0.391387 3_3:-26619779 Msa0447810:CDS
GTTGGCATAGTGACACAAAC+AGG 0.491066 3_3:+26619706 None:intergenic
AATGCTGTCCGAGCAGTTGA+AGG 0.499596 3_3:-26619889 Msa0447810:CDS
GCTTCCCGGCTGTAACCAAC+CGG 0.507766 3_3:-26619951 Msa0447810:CDS
TGCTGTTTGCTCTGTTGCTG+GGG 0.508878 3_3:-26619788 Msa0447810:CDS
AACAACAAAGAGGGCAGCAA+TGG 0.517711 3_3:-26619844 Msa0447810:CDS
TCTTCTCCTCTGCGATGCTA+CGG 0.528081 3_3:+26619924 None:intergenic
AGCCGGGAAGCCGAGGATTG+AGG 0.531969 3_3:+26619963 None:intergenic
TCTGCGATGCTACGGATGAC+CGG 0.544879 3_3:+26619932 None:intergenic
ACAAAGAGGGCAGCAATGGA+AGG 0.546411 3_3:-26619840 Msa0447810:CDS
GATGACCGGTTGGTTACAGC+CGG 0.561463 3_3:+26619946 None:intergenic
ATGCTGTCCGAGCAGTTGAA+GGG 0.565277 3_3:-26619888 Msa0447810:CDS
GCCGAGGATTGAGGATGTCA+TGG 0.565591 3_3:+26619972 None:intergenic
TGGTTACAGCCGGGAAGCCG+AGG 0.566698 3_3:+26619956 None:intergenic
ACCATGACATCCTCAATCCT+CGG 0.573002 3_3:-26619973 Msa0447810:CDS
GTGTCACTATGCCAACAGCT+AGG 0.576409 3_3:-26619699 Msa0447810:CDS
TTGCGACAAATCCTAGCTGT+TGG 0.581063 3_3:+26619688 None:intergenic
TGCTGTCCGAGCAGTTGAAG+GGG 0.590682 3_3:-26619887 Msa0447810:CDS
CGATGCTACGGATGACCGGT+TGG 0.597909 3_3:+26619936 None:intergenic
CAAATATGATAACAACAAAG+AGG 0.606053 3_3:-26619854 Msa0447810:CDS
GCAGATGATGAACCTAAAAG+AGG 0.606913 3_3:-26619757 Msa0447810:CDS
AAATATGATAACAACAAAGA+GGG 0.618750 3_3:-26619853 Msa0447810:CDS
ATGACCGGTTGGTTACAGCC+GGG 0.647755 3_3:+26619947 None:intergenic
GGTCATCCGTAGCATCGCAG+AGG 0.728401 3_3:-26619930 Msa0447810:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATATGATAACAACAAAGA+GGG - chr3_3:26619816-26619835 Msa0447810:CDS 20.0%
! CAAATATGATAACAACAAAG+AGG - chr3_3:26619815-26619834 Msa0447810:CDS 25.0%
!!! ATACTTTTTCTTTGCTTCTG+GGG + chr3_3:26619940-26619959 None:intergenic 30.0%
!!! CATACTTTTTCTTTGCTTCT+GGG + chr3_3:26619941-26619960 None:intergenic 30.0%
!!! GCATACTTTTTCTTTGCTTC+TGG + chr3_3:26619942-26619961 None:intergenic 35.0%
GCAGATGATGAACCTAAAAG+AGG - chr3_3:26619912-26619931 Msa0447810:CDS 40.0%
ACCATGACATCCTCAATCCT+CGG - chr3_3:26619696-26619715 Msa0447810:CDS 45.0%
! TCTTTTCCCCTTCAACTGCT+CGG + chr3_3:26619791-26619810 None:intergenic 45.0%
AACAACAAAGAGGGCAGCAA+TGG - chr3_3:26619825-26619844 Msa0447810:CDS 45.0%
GTTGGCATAGTGACACAAAC+AGG + chr3_3:26619966-26619985 None:intergenic 45.0%
TTGCGACAAATCCTAGCTGT+TGG + chr3_3:26619984-26620003 None:intergenic 45.0%
TCTTCTCCTCTGCGATGCTA+CGG + chr3_3:26619748-26619767 None:intergenic 50.0%
AATGCTGTCCGAGCAGTTGA+AGG - chr3_3:26619780-26619799 Msa0447810:CDS 50.0%
ATGCTGTCCGAGCAGTTGAA+GGG - chr3_3:26619781-26619800 Msa0447810:CDS 50.0%
ACAAAGAGGGCAGCAATGGA+AGG - chr3_3:26619829-26619848 Msa0447810:CDS 50.0%
! CTGCTGTTTGCTCTGTTGCT+GGG - chr3_3:26619880-26619899 Msa0447810:CDS 50.0%
! TGCTGTTTGCTCTGTTGCTG+GGG - chr3_3:26619881-26619900 Msa0447810:CDS 50.0%
!!! GCTTCTGGGGTACCTCTTTT+AGG + chr3_3:26619927-26619946 None:intergenic 50.0%
! GTGTCACTATGCCAACAGCT+AGG - chr3_3:26619970-26619989 Msa0447810:CDS 50.0%
GCCGAGGATTGAGGATGTCA+TGG + chr3_3:26619700-26619719 None:intergenic 55.0%
ATCCTCAATCCTCGGCTTCC+CGG - chr3_3:26619704-26619723 Msa0447810:CDS 55.0%
! ATGACCGGTTGGTTACAGCC+GGG + chr3_3:26619725-26619744 None:intergenic 55.0%
! GATGACCGGTTGGTTACAGC+CGG + chr3_3:26619726-26619745 None:intergenic 55.0%
TCTGCGATGCTACGGATGAC+CGG + chr3_3:26619740-26619759 None:intergenic 55.0%
TGCTGTCCGAGCAGTTGAAG+GGG - chr3_3:26619782-26619801 Msa0447810:CDS 55.0%
! GCTGCTGTTTGCTCTGTTGC+TGG - chr3_3:26619879-26619898 Msa0447810:CDS 55.0%
CTCTGTTGCTGGGGTTGCAA+TGG - chr3_3:26619890-26619909 Msa0447810:CDS 55.0%
GCTTCCCGGCTGTAACCAAC+CGG - chr3_3:26619718-26619737 Msa0447810:CDS 60.0%
CGATGCTACGGATGACCGGT+TGG + chr3_3:26619736-26619755 None:intergenic 60.0%
GGTCATCCGTAGCATCGCAG+AGG - chr3_3:26619739-26619758 Msa0447810:CDS 60.0%
AGCCGGGAAGCCGAGGATTG+AGG + chr3_3:26619709-26619728 None:intergenic 65.0%
TGGTTACAGCCGGGAAGCCG+AGG + chr3_3:26619716-26619735 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 26619684 26620007 26619684 ID=Msa0447810;Name=Msa0447810
chr3_3 mRNA 26619684 26620007 26619684 ID=Msa0447810-mRNA-1;Parent=Msa0447810;Name=Msa0447810-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|107
chr3_3 exon 26619684 26620007 26619684 ID=Msa0447810-mRNA-1:exon:5188;Parent=Msa0447810-mRNA-1
chr3_3 CDS 26619684 26620007 26619684 ID=Msa0447810-mRNA-1:cds;Parent=Msa0447810-mRNA-1
Gene Sequence

>Msa0447810

ATGGCATCAATCACCATGACATCCTCAATCCTCGGCTTCCCGGCTGTAACCAACCGGTCATCCGTAGCATCGCAGAGGAGAAGACTTGTCGTCGTCAATGCTGTCCGAGCAGTTGAAGGGGAAAAGATGATCAAATATGATAACAACAAAGAGGGCAGCAATGGAAGGAGAGACTTGATGTTTGCTGCAGCAGCAGCTGCTGTTTGCTCTGTTGCTGGGGTTGCAATGGCAGATGATGAACCTAAAAGAGGTACCCCAGAAGCAAAGAAAAAGTATGCTCCTGTTTGTGTCACTATGCCAACAGCTAGGATTTGTCGCAATTGA

Protein sequence

>Msa0447810

MASITMTSSILGFPAVTNRSSVASQRRRLVVVNAVRAVEGEKMIKYDNNKEGSNGRRDLMFAAAAAAVCSVAGVAMADDEPKRGTPEAKKKYAPVCVTMPTARICRN*