AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1220770

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1220770 MtrunA17_Chr4g0063391 77.876 113 25 0 1 113 43 155 1.53e-61 187
Msa1220770 MtrunA17_Chr4g0063371 68.000 125 26 2 1 125 51 161 4.88e-54 169
Msa1220770 MtrunA17_Chr4g0063361 61.947 113 43 0 1 113 71 183 2.43e-46 150
Msa1220770 MtrunA17_Chr4g0063401 60.833 120 40 2 1 113 65 184 8.81e-44 143
Msa1220770 MtrunA17_Chr3g0098251 53.636 110 45 2 4 113 25 128 9.60e-35 119
Msa1220770 MtrunA17_Chr8g0360671 55.000 80 30 2 34 113 40 113 2.15e-23 89.0
Msa1220770 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
Msa1220770 AT3G19360.1 47.287 129 49 1 4 113 95 223 7.33e-34 121
Msa1220770 AT3G19360.2 47.287 129 49 1 4 113 95 223 7.33e-34 121
Msa1220770 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:-84075689 None:intergenic
ACTTATCGGAACTAATAATT+TGG 0.230797 8_1:+84075891 Msa1220770:CDS
ATGAAGATCCTGCACAGTTT+AGG 0.265678 8_1:+84075843 Msa1220770:CDS
TGAAGATCCTGCACAGTTTA+GGG 0.304032 8_1:+84075844 Msa1220770:CDS
AATTTACAGTTATCTCTATA+TGG 0.333739 8_1:-84075815 None:intergenic
TAAGTACTCTCTTGATTTCA+AGG 0.365996 8_1:-84075873 None:intergenic
ATTTGTACCGAGTTCAGATT+TGG 0.381030 8_1:+84075602 Msa1220770:CDS
GAAATCAAGAGAGTACTTAT+CGG 0.430920 8_1:+84075877 Msa1220770:CDS
AGATTTGGTGCTTGTAGAAA+CGG 0.437088 8_1:+84075617 Msa1220770:CDS
CAACGAAGATCAACTGCAGC+TGG 0.445811 8_1:+84075718 Msa1220770:CDS
CTAATAATTTGGAAGGCAGC+AGG 0.471854 8_1:+84075902 Msa1220770:CDS
AGCTTCTGCAAATTTGGTGG+TGG 0.473172 8_1:-84075683 None:intergenic
TGTGCAAGAAGTATTGCAAT+GGG 0.488339 8_1:+84075783 Msa1220770:CDS
TGCTCTGATTTGTTTGATTG+AGG 0.510278 8_1:-84075560 None:intergenic
CCTAGCTTCTGCAAATTTGG+TGG 0.512657 8_1:-84075686 None:intergenic
TGCAGTTGATCTTCGTTGCA+CGG 0.530704 8_1:-84075713 None:intergenic
ATCATGGAGCTGAAGAGATA+AGG 0.532117 8_1:+84075657 Msa1220770:CDS
GAATCATCCCTAAACTGTGC+AGG 0.539981 8_1:-84075851 None:intergenic
ATCGGAACTAATAATTTGGA+AGG 0.541233 8_1:+84075895 Msa1220770:CDS
TGATTTGTTTGATTGAGGCA+AGG 0.569543 8_1:-84075555 None:intergenic
CTGTGCAAGAAGTATTGCAA+TGG 0.572239 8_1:+84075782 Msa1220770:CDS
TAATAATTTGGAAGGCAGCA+GGG 0.584634 8_1:+84075903 Msa1220770:CDS
AACGAAGATCAACTGCAGCT+GGG 0.593604 8_1:+84075719 Msa1220770:CDS
ACTGTGCAGGATCTTCATGA+AGG 0.599205 8_1:-84075838 None:intergenic
CCACCAAATTTGCAGAAGCT+AGG 0.604649 8_1:+84075686 Msa1220770:CDS
CCAAATTTGCAGAAGCTAGG+TGG 0.641093 8_1:+84075689 Msa1220770:CDS
CAAGAAGTATTGCAATGGGG+AGG 0.655957 8_1:+84075787 Msa1220770:CDS
ACAAGCACCAAATCTGAACT+CGG 0.659308 8_1:-84075609 None:intergenic
GTGCAAGAAGTATTGCAATG+GGG 0.763140 8_1:+84075784 Msa1220770:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGATGAAAAAATCATACAA+AGG + chr8_1:84075753-84075772 Msa1220770:CDS 20.0%
!! AATTTACAGTTATCTCTATA+TGG - chr8_1:84075818-84075837 None:intergenic 20.0%
! AAAAATTGCAACTTTGATCA+TGG + chr8_1:84075641-84075660 Msa1220770:CDS 25.0%
! ACTTATCGGAACTAATAATT+TGG + chr8_1:84075891-84075910 Msa1220770:CDS 25.0%
TAAGTACTCTCTTGATTTCA+AGG - chr8_1:84075876-84075895 None:intergenic 30.0%
!! GAAATCAAGAGAGTACTTAT+CGG + chr8_1:84075877-84075896 Msa1220770:CDS 30.0%
ATCGGAACTAATAATTTGGA+AGG + chr8_1:84075895-84075914 Msa1220770:CDS 30.0%
!! TGATTTGTTTGATTGAGGCA+AGG - chr8_1:84075558-84075577 None:intergenic 35.0%
!! TGCTCTGATTTGTTTGATTG+AGG - chr8_1:84075563-84075582 None:intergenic 35.0%
ATTTGTACCGAGTTCAGATT+TGG + chr8_1:84075602-84075621 Msa1220770:CDS 35.0%
!! AGATTTGGTGCTTGTAGAAA+CGG + chr8_1:84075617-84075636 Msa1220770:CDS 35.0%
!! TGTGCAAGAAGTATTGCAAT+GGG + chr8_1:84075783-84075802 Msa1220770:CDS 35.0%
TAATAATTTGGAAGGCAGCA+GGG + chr8_1:84075903-84075922 Msa1220770:CDS 35.0%
ACAAGCACCAAATCTGAACT+CGG - chr8_1:84075612-84075631 None:intergenic 40.0%
ATCATGGAGCTGAAGAGATA+AGG + chr8_1:84075657-84075676 Msa1220770:CDS 40.0%
!! CTGTGCAAGAAGTATTGCAA+TGG + chr8_1:84075782-84075801 Msa1220770:CDS 40.0%
!! GTGCAAGAAGTATTGCAATG+GGG + chr8_1:84075784-84075803 Msa1220770:CDS 40.0%
ATGAAGATCCTGCACAGTTT+AGG + chr8_1:84075843-84075862 Msa1220770:CDS 40.0%
TGAAGATCCTGCACAGTTTA+GGG + chr8_1:84075844-84075863 Msa1220770:CDS 40.0%
CTAATAATTTGGAAGGCAGC+AGG + chr8_1:84075902-84075921 Msa1220770:CDS 40.0%
! AGCTTCTGCAAATTTGGTGG+TGG - chr8_1:84075686-84075705 None:intergenic 45.0%
CCTAGCTTCTGCAAATTTGG+TGG - chr8_1:84075689-84075708 None:intergenic 45.0%
CCACCAAATTTGCAGAAGCT+AGG + chr8_1:84075686-84075705 Msa1220770:CDS 45.0%
CCACCTAGCTTCTGCAAATT+TGG - chr8_1:84075692-84075711 None:intergenic 45.0%
CCAAATTTGCAGAAGCTAGG+TGG + chr8_1:84075689-84075708 Msa1220770:CDS 45.0%
TGCAGTTGATCTTCGTTGCA+CGG - chr8_1:84075716-84075735 None:intergenic 45.0%
AACGAAGATCAACTGCAGCT+GGG + chr8_1:84075719-84075738 Msa1220770:CDS 45.0%
!! CAAGAAGTATTGCAATGGGG+AGG + chr8_1:84075787-84075806 Msa1220770:CDS 45.0%
ACTGTGCAGGATCTTCATGA+AGG - chr8_1:84075841-84075860 None:intergenic 45.0%
GAATCATCCCTAAACTGTGC+AGG - chr8_1:84075854-84075873 None:intergenic 45.0%
CAACGAAGATCAACTGCAGC+TGG + chr8_1:84075718-84075737 Msa1220770:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 84075551 84075931 84075551 ID=Msa1220770;Name=Msa1220770
chr8_1 mRNA 84075551 84075931 84075551 ID=Msa1220770-mRNA-1;Parent=Msa1220770;Name=Msa1220770-mRNA-1;_AED=0.39;_eAED=0.41;_QI=0|-1|0|1|-1|1|1|0|126
chr8_1 exon 84075551 84075931 84075551 ID=Msa1220770-mRNA-1:exon:30153;Parent=Msa1220770-mRNA-1
chr8_1 CDS 84075551 84075931 84075551 ID=Msa1220770-mRNA-1:cds;Parent=Msa1220770-mRNA-1
Gene Sequence

>Msa1220770

ATGGCCTTGCCTCAATCAAACAAATCAGAGCACATTTTTTACAAAACACGAATTTGTACCGAGTTCAGATTTGGTGCTTGTAGAAACGGAAAAAATTGCAACTTTGATCATGGAGCTGAAGAGATAAGGCAACCACCACCAAATTTGCAGAAGCTAGGTGGTCCGTGCAACGAAGATCAACTGCAGCTGGGAAATCAAGTTGAAGATGAAAAAATCATACAAAGGATGAAACTGTGCAAGAAGTATTGCAATGGGGAGGAATGTCCATATAGAGATAACTGTAAATTCCTTCATGAAGATCCTGCACAGTTTAGGGATGATTCCTTGAAATCAAGAGAGTACTTATCGGAACTAATAATTTGGAAGGCAGCAGGGCTGTGA
Protein sequence

>Msa1220770

MALPQSNKSEHIFYKTRICTEFRFGACRNGKNCNFDHGAEEIRQPPPNLQKLGGPCNEDQLQLGNQVEDEKIIQRMKLCKKYCNGEECPYRDNCKFLHEDPAQFRDDSLKSREYLSELIIWKAAGL*