AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1220790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1220790 MtrunA17_Chr4g0063391 77.876 113 25 0 1 113 43 155 1.53e-61 187
Msa1220790 MtrunA17_Chr4g0063371 68.000 125 26 2 1 125 51 161 4.88e-54 169
Msa1220790 MtrunA17_Chr4g0063361 61.947 113 43 0 1 113 71 183 2.43e-46 150
Msa1220790 MtrunA17_Chr4g0063401 60.833 120 40 2 1 113 65 184 8.81e-44 143
Msa1220790 MtrunA17_Chr3g0098251 53.636 110 45 2 4 113 25 128 9.60e-35 119
Msa1220790 MtrunA17_Chr8g0360671 55.000 80 30 2 34 113 40 113 2.15e-23 89.0
Msa1220790 MtrunA17_Chr8g0366501 32.432 111 59 1 12 106 91 201 2.73e-14 67.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1220790 AT3G19360.1 47.287 129 49 1 4 113 95 223 7.33e-34 121
Msa1220790 AT3G19360.2 47.287 129 49 1 4 113 95 223 7.33e-34 121
Msa1220790 AT1G32360.1 32.759 116 57 3 12 106 90 205 8.23e-15 69.7

Find 29 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCACCTAGCTTCTGCAAATT+TGG 0.182814 8_1:-84117759 None:intergenic
ACTTATCGGAACTAATAATT+TGG 0.230797 8_1:+84117961 Msa1220790:CDS
ATGAAGATCCTGCACAGTTT+AGG 0.265678 8_1:+84117913 Msa1220790:CDS
TGAAGATCCTGCACAGTTTA+GGG 0.304032 8_1:+84117914 Msa1220790:CDS
AATTTACAGTTATCTCTATA+TGG 0.333739 8_1:-84117885 None:intergenic
TAAGTACTCTCTTGATTTCA+AGG 0.365996 8_1:-84117943 None:intergenic
ATTTGTACCGAGTTCAGATT+TGG 0.381030 8_1:+84117672 Msa1220790:CDS
GAAATCAAGAGAGTACTTAT+CGG 0.430920 8_1:+84117947 Msa1220790:CDS
AGATTTGGTGCTTGTAGAAA+CGG 0.437088 8_1:+84117687 Msa1220790:CDS
CAACGAAGATCAACTGCAGC+TGG 0.445811 8_1:+84117788 Msa1220790:CDS
CTAATAATTTGGAAGGCAGC+AGG 0.471854 8_1:+84117972 Msa1220790:CDS
AGCTTCTGCAAATTTGGTGG+TGG 0.473172 8_1:-84117753 None:intergenic
TGTGCAAGAAGTATTGCAAT+GGG 0.488339 8_1:+84117853 Msa1220790:CDS
TGCTCTGATTTGTTTGATTG+AGG 0.510278 8_1:-84117630 None:intergenic
CCTAGCTTCTGCAAATTTGG+TGG 0.512657 8_1:-84117756 None:intergenic
TGCAGTTGATCTTCGTTGCA+CGG 0.530704 8_1:-84117783 None:intergenic
ATCATGGAGCTGAAGAGATA+AGG 0.532117 8_1:+84117727 Msa1220790:CDS
GAATCATCCCTAAACTGTGC+AGG 0.539981 8_1:-84117921 None:intergenic
ATCGGAACTAATAATTTGGA+AGG 0.541233 8_1:+84117965 Msa1220790:CDS
TGATTTGTTTGATTGAGGCA+AGG 0.569543 8_1:-84117625 None:intergenic
CTGTGCAAGAAGTATTGCAA+TGG 0.572239 8_1:+84117852 Msa1220790:CDS
TAATAATTTGGAAGGCAGCA+GGG 0.584634 8_1:+84117973 Msa1220790:CDS
AACGAAGATCAACTGCAGCT+GGG 0.593604 8_1:+84117789 Msa1220790:CDS
ACTGTGCAGGATCTTCATGA+AGG 0.599205 8_1:-84117908 None:intergenic
CCACCAAATTTGCAGAAGCT+AGG 0.604649 8_1:+84117756 Msa1220790:CDS
CCAAATTTGCAGAAGCTAGG+TGG 0.641093 8_1:+84117759 Msa1220790:CDS
CAAGAAGTATTGCAATGGGG+AGG 0.655957 8_1:+84117857 Msa1220790:CDS
ACAAGCACCAAATCTGAACT+CGG 0.659308 8_1:-84117679 None:intergenic
GTGCAAGAAGTATTGCAATG+GGG 0.763140 8_1:+84117854 Msa1220790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGATGAAAAAATCATACAA+AGG + chr8_1:84117823-84117842 Msa1220790:CDS 20.0%
!! AATTTACAGTTATCTCTATA+TGG - chr8_1:84117888-84117907 None:intergenic 20.0%
! AAAAATTGCAACTTTGATCA+TGG + chr8_1:84117711-84117730 Msa1220790:CDS 25.0%
! ACTTATCGGAACTAATAATT+TGG + chr8_1:84117961-84117980 Msa1220790:CDS 25.0%
TAAGTACTCTCTTGATTTCA+AGG - chr8_1:84117946-84117965 None:intergenic 30.0%
!! GAAATCAAGAGAGTACTTAT+CGG + chr8_1:84117947-84117966 Msa1220790:CDS 30.0%
ATCGGAACTAATAATTTGGA+AGG + chr8_1:84117965-84117984 Msa1220790:CDS 30.0%
!! TGATTTGTTTGATTGAGGCA+AGG - chr8_1:84117628-84117647 None:intergenic 35.0%
!! TGCTCTGATTTGTTTGATTG+AGG - chr8_1:84117633-84117652 None:intergenic 35.0%
ATTTGTACCGAGTTCAGATT+TGG + chr8_1:84117672-84117691 Msa1220790:CDS 35.0%
!! AGATTTGGTGCTTGTAGAAA+CGG + chr8_1:84117687-84117706 Msa1220790:CDS 35.0%
!! TGTGCAAGAAGTATTGCAAT+GGG + chr8_1:84117853-84117872 Msa1220790:CDS 35.0%
TAATAATTTGGAAGGCAGCA+GGG + chr8_1:84117973-84117992 Msa1220790:CDS 35.0%
ACAAGCACCAAATCTGAACT+CGG - chr8_1:84117682-84117701 None:intergenic 40.0%
ATCATGGAGCTGAAGAGATA+AGG + chr8_1:84117727-84117746 Msa1220790:CDS 40.0%
!! CTGTGCAAGAAGTATTGCAA+TGG + chr8_1:84117852-84117871 Msa1220790:CDS 40.0%
!! GTGCAAGAAGTATTGCAATG+GGG + chr8_1:84117854-84117873 Msa1220790:CDS 40.0%
ATGAAGATCCTGCACAGTTT+AGG + chr8_1:84117913-84117932 Msa1220790:CDS 40.0%
TGAAGATCCTGCACAGTTTA+GGG + chr8_1:84117914-84117933 Msa1220790:CDS 40.0%
CTAATAATTTGGAAGGCAGC+AGG + chr8_1:84117972-84117991 Msa1220790:CDS 40.0%
! AGCTTCTGCAAATTTGGTGG+TGG - chr8_1:84117756-84117775 None:intergenic 45.0%
CCTAGCTTCTGCAAATTTGG+TGG - chr8_1:84117759-84117778 None:intergenic 45.0%
CCACCAAATTTGCAGAAGCT+AGG + chr8_1:84117756-84117775 Msa1220790:CDS 45.0%
CCACCTAGCTTCTGCAAATT+TGG - chr8_1:84117762-84117781 None:intergenic 45.0%
CCAAATTTGCAGAAGCTAGG+TGG + chr8_1:84117759-84117778 Msa1220790:CDS 45.0%
TGCAGTTGATCTTCGTTGCA+CGG - chr8_1:84117786-84117805 None:intergenic 45.0%
AACGAAGATCAACTGCAGCT+GGG + chr8_1:84117789-84117808 Msa1220790:CDS 45.0%
!! CAAGAAGTATTGCAATGGGG+AGG + chr8_1:84117857-84117876 Msa1220790:CDS 45.0%
ACTGTGCAGGATCTTCATGA+AGG - chr8_1:84117911-84117930 None:intergenic 45.0%
GAATCATCCCTAAACTGTGC+AGG - chr8_1:84117924-84117943 None:intergenic 45.0%
CAACGAAGATCAACTGCAGC+TGG + chr8_1:84117788-84117807 Msa1220790:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 84117621 84118001 84117621 ID=Msa1220790;Name=Msa1220790
chr8_1 mRNA 84117621 84118001 84117621 ID=Msa1220790-mRNA-1;Parent=Msa1220790;Name=Msa1220790-mRNA-1;_AED=0.43;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|126
chr8_1 exon 84117621 84118001 84117621 ID=Msa1220790-mRNA-1:exon:30210;Parent=Msa1220790-mRNA-1
chr8_1 CDS 84117621 84118001 84117621 ID=Msa1220790-mRNA-1:cds;Parent=Msa1220790-mRNA-1
Gene Sequence

>Msa1220790

ATGGCCTTGCCTCAATCAAACAAATCAGAGCACATTTTTTACAAAACACGAATTTGTACCGAGTTCAGATTTGGTGCTTGTAGAAACGGAAAAAATTGCAACTTTGATCATGGAGCTGAAGAGATAAGGCAACCACCACCAAATTTGCAGAAGCTAGGTGGTCCGTGCAACGAAGATCAACTGCAGCTGGGAAATCAAGTTGAAGATGAAAAAATCATACAAAGGATGAAACTGTGCAAGAAGTATTGCAATGGGGAGGAATGTCCATATAGAGATAACTGTAAATTCCTTCATGAAGATCCTGCACAGTTTAGGGATGATTCCTTGAAATCAAGAGAGTACTTATCGGAACTAATAATTTGGAAGGCAGCAGGGCTGTGA
Protein sequence

>Msa1220790

MALPQSNKSEHIFYKTRICTEFRFGACRNGKNCNFDHGAEEIRQPPPNLQKLGGPCNEDQLQLGNQVEDEKIIQRMKLCKKYCNGEECPYRDNCKFLHEDPAQFRDDSLKSREYLSELIIWKAAGL*