AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0538240


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0538240 MtrunA17_Chr4g0012941 54.795 73 6 1 42 87 7 79 7.18e-18 72.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACTGCTTCACAACAATA+TGG 0.222130 4_1:+17410157 None:intergenic
GAATACCACACAAGGCAAAT+AGG 0.325859 4_1:+17410021 None:intergenic
AATCTATCAGCTTCTGCAAT+AGG 0.389891 4_1:+17410247 None:intergenic
AGTAAGAGTATAAATAATAA+AGG 0.397290 4_1:+17410222 None:intergenic
AATACCACACAAGGCAAATA+GGG 0.412629 4_1:+17410022 None:intergenic
GGTCGTTGCATGTCTCGTTT+TGG 0.415995 4_1:-17410290 Msa0538240:CDS
GAAATATAACCTTGAAGAAA+AGG 0.420263 4_1:+17410190 None:intergenic
TGGTTATATTTACAGAATCA+AGG 0.425590 4_1:-17407811 Msa0538240:intron
AGTTGATATCGCGAGTAATC+TGG 0.431895 4_1:+17409988 None:intergenic
GTGGAAGTTGTGGCGGATGT+TGG 0.448150 4_1:-17407786 Msa0538240:CDS
TCACTGCTTCACAACAATAT+GGG 0.474158 4_1:+17410158 None:intergenic
CAATAAAGCACTCTATATAG+TGG 0.508786 4_1:+17407746 None:intergenic
GGTTATATTTACAGAATCAA+GGG 0.515885 4_1:-17407810 Msa0538240:intron
CCTTGAAGAAAAGGATAGCA+TGG 0.525784 4_1:+17410199 None:intergenic
AAGACTTTGAATGTGGAGAA+TGG 0.533346 4_1:-17410050 Msa0538240:CDS
TTCTTTAAAGACTTTGAATG+TGG 0.543973 4_1:-17410057 Msa0538240:intron
AATCAAGGGTGTGGAAGTTG+TGG 0.551229 4_1:-17407796 Msa0538240:CDS
TATTTACAGAATCAAGGGTG+TGG 0.556405 4_1:-17407805 Msa0538240:intron
TTGTGGCGGATGTTGGATCA+AGG 0.564536 4_1:-17407779 Msa0538240:CDS
GCTGCCCTATTTGCCTTGTG+TGG 0.597976 4_1:-17410026 Msa0538240:CDS
GATATCGCGAGTAATCTGGT+AGG 0.618889 4_1:+17409992 None:intergenic
ATATCGCGAGTAATCTGGTA+GGG 0.629903 4_1:+17409993 None:intergenic
CAAGGGTGTGGAAGTTGTGG+CGG 0.655854 4_1:-17407793 Msa0538240:CDS
GGGTGTTTGAATACCACACA+AGG 0.676879 4_1:+17410013 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCATATAATATAATCTATT+TGG - chr4_1:17408168-17408187 Msa0538240:intron 10.0%
!! TAAAATAAACAATTTAGTTA+AGG - chr4_1:17408977-17408996 Msa0538240:intron 10.0%
!!! TTTATCTAAATTCATTTTTA+AGG + chr4_1:17409136-17409155 None:intergenic 10.0%
!! AAAATATAGTAAAATATATC+AGG + chr4_1:17409254-17409273 None:intergenic 10.0%
!! TAAATTATCCTTAAAAAAAA+AGG + chr4_1:17409322-17409341 None:intergenic 10.0%
!!! TTTTTTTTAACAAACAAAAA+TGG + chr4_1:17409693-17409712 None:intergenic 10.0%
!!! AGTAAGAGTATAAATAATAA+AGG + chr4_1:17407819-17407838 None:intergenic 15.0%
!!! AGATTGTTGATTATTATTTT+TGG - chr4_1:17408598-17408617 Msa0538240:intron 15.0%
!!! TTGATTTTTTTTTCTTTTCT+GGG - chr4_1:17408644-17408663 Msa0538240:intron 15.0%
!! AAAATTAATAAAGTATATGG+TGG - chr4_1:17408827-17408846 Msa0538240:intron 15.0%
!! TAACCTTAAATATCTAATAT+GGG + chr4_1:17408870-17408889 None:intergenic 15.0%
!! TTAACCTTAAATATCTAATA+TGG + chr4_1:17408871-17408890 None:intergenic 15.0%
!! TAATTTGACAGAAAATATAT+TGG - chr4_1:17409071-17409090 Msa0538240:intron 15.0%
!! TAAAATATATCAGGAAATAA+CGG + chr4_1:17409245-17409264 None:intergenic 15.0%
!!! TACTTTTGTTGATTATTTAA+TGG - chr4_1:17409976-17409995 Msa0538240:intron 15.0%
!! ATTAATAAATTTCTTACCTT+TGG + chr4_1:17410195-17410214 None:intergenic 15.0%
!!! TTATTAATGACTTCTTTTAT+TGG - chr4_1:17410207-17410226 Msa0538240:CDS 15.0%
!! TCAATGTTATGTTATTGTTA+TGG + chr4_1:17408125-17408144 None:intergenic 20.0%
!! AATCTCGTTTATATATTAGT+TGG - chr4_1:17408375-17408394 Msa0538240:intron 20.0%
!!! GTTGATTTTTTTTTCTTTTC+TGG - chr4_1:17408643-17408662 Msa0538240:intron 20.0%
!!! ATTTAAGGTTAAAGTGTTAA+CGG - chr4_1:17408879-17408898 Msa0538240:intron 20.0%
!! ATTATGCCTAAAAAATTTGA+AGG - chr4_1:17409012-17409031 Msa0538240:intron 20.0%
!!! TCATTTTTAAGGATTTGATA+GGG + chr4_1:17409125-17409144 None:intergenic 20.0%
!!! TTCATTTTTAAGGATTTGAT+AGG + chr4_1:17409126-17409145 None:intergenic 20.0%
!! ATACCAATATTGCAATTAAT+CGG - chr4_1:17409157-17409176 Msa0538240:intron 20.0%
!! AAAATATATCAGGAAATAAC+GGG + chr4_1:17409244-17409263 None:intergenic 20.0%
!!! TCTTTCATCCTTTTTTTTTA+AGG - chr4_1:17409311-17409330 Msa0538240:intron 20.0%
!!! TGAAATGAGTCAATTATTTT+AGG + chr4_1:17409508-17409527 None:intergenic 20.0%
!! AATTCAAAGACAATCTTTAT+TGG - chr4_1:17409939-17409958 Msa0538240:intron 20.0%
!! ATTCAAAGACAATCTTTATT+GGG - chr4_1:17409940-17409959 Msa0538240:intron 20.0%
!!! ATAAAGCTAGAGTTTTTTTA+GGG + chr4_1:17410118-17410137 None:intergenic 20.0%
!!! CAATTTTGAAAATAAATCCT+AGG + chr4_1:17410151-17410170 None:intergenic 20.0%
!!! TAGTTAATGAATTTTTCCAA+AGG - chr4_1:17410176-17410195 Msa0538240:CDS 20.0%
! GAAATATAACCTTGAAGAAA+AGG + chr4_1:17407851-17407870 None:intergenic 25.0%
!! TTCTTTAAAGACTTTGAATG+TGG - chr4_1:17407981-17408000 Msa0538240:intron 25.0%
!! TTAGTGAAAGTATACATACT+TGG + chr4_1:17408079-17408098 None:intergenic 25.0%
! TCGTTTATATATTAGTTGGT+AGG - chr4_1:17408379-17408398 Msa0538240:intron 25.0%
! TAATATAATATGCAGCACAA+CGG + chr4_1:17408548-17408567 None:intergenic 25.0%
!!! TTTTTTTTTCTTTTCTGGGT+AGG - chr4_1:17408648-17408667 Msa0538240:intron 25.0%
! AGGGAAAAATTAGATATTGA+TGG - chr4_1:17408728-17408747 Msa0538240:intron 25.0%
!! AATTAGATATTGATGGTTCA+CGG - chr4_1:17408735-17408754 Msa0538240:intron 25.0%
!!! TTTTTTAAAAAGAAGACCGT+TGG + chr4_1:17408785-17408804 None:intergenic 25.0%
!! ATATGGGCTAAAATTAAAAG+TGG + chr4_1:17408854-17408873 None:intergenic 25.0%
! TAGCCCATATTAGATATTTA+AGG - chr4_1:17408864-17408883 Msa0538240:intron 25.0%
! TTTCTTGCCTTTATATGTTA+TGG + chr4_1:17408911-17408930 None:intergenic 25.0%
! CTAAAAAAAACTTCTCAAAG+TGG + chr4_1:17408943-17408962 None:intergenic 25.0%
!!! TGAGAAGTTTTTTTTAGTCA+AGG - chr4_1:17408946-17408965 Msa0538240:intron 25.0%
!!! GAGAAGTTTTTTTTAGTCAA+GGG - chr4_1:17408947-17408966 Msa0538240:intron 25.0%
!!! TTCATGCCTTCAAATTTTTT+AGG + chr4_1:17409021-17409040 None:intergenic 25.0%
! TATCCGATTAATTGCAATAT+TGG + chr4_1:17409163-17409182 None:intergenic 25.0%
! GTCAAGGAGTTATATATTTA+GGG + chr4_1:17409361-17409380 None:intergenic 25.0%
! AGTCAAGGAGTTATATATTT+AGG + chr4_1:17409362-17409381 None:intergenic 25.0%
! CCATGAAAGAATTAAAGATA+CGG - chr4_1:17409409-17409428 Msa0538240:intron 25.0%
! AAATACACTAATACTTGACA+AGG - chr4_1:17409771-17409790 Msa0538240:intron 25.0%
! AATACACTAATACTTGACAA+GGG - chr4_1:17409772-17409791 Msa0538240:intron 25.0%
! AAGAAAAATGTACTAGTGAA+GGG + chr4_1:17409820-17409839 None:intergenic 25.0%
! TAAGAAAAATGTACTAGTGA+AGG + chr4_1:17409821-17409840 None:intergenic 25.0%
! AAAACTCACTTAAATTGAGA+CGG - chr4_1:17409861-17409880 Msa0538240:intron 25.0%
!! TTTAAGATTGAGTCACTATT+TGG - chr4_1:17410045-17410064 Msa0538240:CDS 25.0%
!!! TAAAGCTAGAGTTTTTTTAG+GGG + chr4_1:17410117-17410136 None:intergenic 25.0%
!!! GATAAAGCTAGAGTTTTTTT+AGG + chr4_1:17410119-17410138 None:intergenic 25.0%
! TGGTTATATTTACAGAATCA+AGG - chr4_1:17410227-17410246 Msa0538240:CDS 25.0%
! GGTTATATTTACAGAATCAA+GGG - chr4_1:17410228-17410247 Msa0538240:CDS 25.0%
! ACTTGTGCTTTATGAGATTT+TGG - chr4_1:17408478-17408497 Msa0538240:intron 30.0%
! TTTATGAGATTTTGGACCAA+GGG - chr4_1:17408486-17408505 Msa0538240:intron 30.0%
AATATAATATGCAGCACAAC+GGG + chr4_1:17408547-17408566 None:intergenic 30.0%
!! TATTTTGGGTATGAAGTTGA+AGG - chr4_1:17408572-17408591 Msa0538240:intron 30.0%
AGTAAGAAGATGAAGAAAAG+AGG - chr4_1:17408708-17408727 Msa0538240:intron 30.0%
GTAAGAAGATGAAGAAAAGA+GGG - chr4_1:17408709-17408728 Msa0538240:intron 30.0%
CATATAAAGGCAAGAAACTT+AGG - chr4_1:17408914-17408933 Msa0538240:intron 30.0%
ATAACTCCTTGACTAAATGA+TGG - chr4_1:17409368-17409387 Msa0538240:CDS 30.0%
TAACTCCTTGACTAAATGAT+GGG - chr4_1:17409369-17409388 Msa0538240:CDS 30.0%
AAATTCCCATCATTTAGTCA+AGG + chr4_1:17409377-17409396 None:intergenic 30.0%
CCGTATCTTTAATTCTTTCA+TGG + chr4_1:17409412-17409431 None:intergenic 30.0%
ACAAGAGACTCACTTATTAA+GGG + chr4_1:17409473-17409492 None:intergenic 30.0%
TACAAGAGACTCACTTATTA+AGG + chr4_1:17409474-17409493 None:intergenic 30.0%
AGAAAAATGTACTAGTGAAG+GGG + chr4_1:17409819-17409838 None:intergenic 30.0%
AAAGACAATCTTTATTGGGA+CGG - chr4_1:17409944-17409963 Msa0538240:intron 30.0%
!! GCTTTATCGTTTTTATTCCT+AGG - chr4_1:17410131-17410150 Msa0538240:intron 30.0%
! CAATAAAGCACTCTATATAG+TGG + chr4_1:17410295-17410314 None:intergenic 30.0%
AATCTATCAGCTTCTGCAAT+AGG + chr4_1:17407794-17407813 None:intergenic 35.0%
TCACTGCTTCACAACAATAT+GGG + chr4_1:17407883-17407902 None:intergenic 35.0%
TTCACTGCTTCACAACAATA+TGG + chr4_1:17407884-17407903 None:intergenic 35.0%
AAGACTTTGAATGTGGAGAA+TGG - chr4_1:17407988-17408007 Msa0538240:intron 35.0%
AATACCACACAAGGCAAATA+GGG + chr4_1:17408019-17408038 None:intergenic 35.0%
! CTTTATGAGATTTTGGACCA+AGG - chr4_1:17408485-17408504 Msa0538240:intron 35.0%
GAGAGGACCATAACATATAA+AGG - chr4_1:17408901-17408920 Msa0538240:intron 35.0%
!! CAAGAGTATTTACAAGGAGA+AGG + chr4_1:17409610-17409629 None:intergenic 35.0%
TCCTTGTAAATACTCTTGAG+TGG - chr4_1:17409612-17409631 Msa0538240:intron 35.0%
!! ACCACTCAAGAGTATTTACA+AGG + chr4_1:17409616-17409635 None:intergenic 35.0%
!! AACTAATACTTCTGAGACAC+TGG + chr4_1:17410012-17410031 None:intergenic 35.0%
TATTTACAGAATCAAGGGTG+TGG - chr4_1:17410233-17410252 Msa0538240:CDS 35.0%
CCTTGAAGAAAAGGATAGCA+TGG + chr4_1:17407842-17407861 None:intergenic 40.0%
! CCATGCTATCCTTTTCTTCA+AGG - chr4_1:17407839-17407858 Msa0538240:intron 40.0%
TAGACGATCATCATAGTCGA+TGG + chr4_1:17407924-17407943 None:intergenic 40.0%
TTGTGACTGCTTGAGAGATA+TGG - chr4_1:17407949-17407968 Msa0538240:intron 40.0%
GAATACCACACAAGGCAAAT+AGG + chr4_1:17408020-17408039 None:intergenic 40.0%
ATATCGCGAGTAATCTGGTA+GGG + chr4_1:17408048-17408067 None:intergenic 40.0%
! AGTTGATATCGCGAGTAATC+TGG + chr4_1:17408053-17408072 None:intergenic 40.0%
AATAGAGTTGCACGATCCAA+CGG - chr4_1:17408766-17408785 Msa0538240:intron 40.0%
! AGGTTAAAGTGTTAACGGAG+AGG - chr4_1:17408884-17408903 Msa0538240:intron 40.0%
ACTCACTTATTAAGGGACGA+AGG + chr4_1:17409466-17409485 None:intergenic 40.0%
!! TACAAGGAGAAGGTGCTAAA+AGG + chr4_1:17409600-17409619 None:intergenic 40.0%
TAGTGAAGGGGAGAGAAAAA+TGG + chr4_1:17409807-17409826 None:intergenic 40.0%
ACTCACTTAAATTGAGACGG+AGG - chr4_1:17409864-17409883 Msa0538240:intron 40.0%
CTCACTTAAATTGAGACGGA+GGG - chr4_1:17409865-17409884 Msa0538240:intron 40.0%
GGGTGTTTGAATACCACACA+AGG + chr4_1:17408028-17408047 None:intergenic 45.0%
GATATCGCGAGTAATCTGGT+AGG + chr4_1:17408049-17408068 None:intergenic 45.0%
GGACCAAGGGATTTCGAAAA+CGG - chr4_1:17408499-17408518 Msa0538240:intron 45.0%
GACCAAGGGATTTCGAAAAC+GGG - chr4_1:17408500-17408519 Msa0538240:intron 45.0%
!! GAGAAGGTGCTAAAAGGAGA+AGG + chr4_1:17409594-17409613 None:intergenic 45.0%
! AATCAAGGGTGTGGAAGTTG+TGG - chr4_1:17410242-17410261 Msa0538240:CDS 45.0%
!! AAAAAAAATATATAATCTAT+AGG - chr4_1:17408193-17408212 Msa0538240:intron 5.0%
!!! ATATTATATTATGTTTATTT+TGG - chr4_1:17408557-17408576 Msa0538240:intron 5.0%
!!! TATTATATTATGTTTATTTT+GGG - chr4_1:17408558-17408577 Msa0538240:intron 5.0%
!! AAAAAAATTAATAAAGTATA+TGG - chr4_1:17408824-17408843 Msa0538240:intron 5.0%
!!! ATAAAATTTAGATTTTTTTT+TGG - chr4_1:17409275-17409294 Msa0538240:intron 5.0%
! GGTCGTTGCATGTCTCGTTT+TGG - chr4_1:17407748-17407767 Msa0538240:exon 50.0%
! CTCCCGTTTTCGAAATCCCT+TGG + chr4_1:17408505-17408524 None:intergenic 50.0%
!! TTGTGGCGGATGTTGGATCA+AGG - chr4_1:17410259-17410278 Msa0538240:CDS 50.0%
GCTGCCCTATTTGCCTTGTG+TGG - chr4_1:17408012-17408031 Msa0538240:intron 55.0%
CCGCACAAGGCGTGCTAAAA+GGG + chr4_1:17409641-17409660 None:intergenic 55.0%
! CCCTTTTAGCACGCCTTGTG+CGG - chr4_1:17409638-17409657 Msa0538240:intron 55.0%
! CCTTTTAGCACGCCTTGTGC+GGG - chr4_1:17409639-17409658 Msa0538240:intron 55.0%
! CTTTTAGCACGCCTTGTGCG+GGG - chr4_1:17409640-17409659 Msa0538240:intron 55.0%
! TTTTAGCACGCCTTGTGCGG+GGG - chr4_1:17409641-17409660 Msa0538240:intron 55.0%
TAGCAGATAACCCCCGCACA+AGG + chr4_1:17409654-17409673 None:intergenic 55.0%
! CAAGGGTGTGGAAGTTGTGG+CGG - chr4_1:17410245-17410264 Msa0538240:CDS 55.0%
!! GTGGAAGTTGTGGCGGATGT+TGG - chr4_1:17410252-17410271 Msa0538240:CDS 55.0%
CCCGCACAAGGCGTGCTAAA+AGG + chr4_1:17409642-17409661 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 17407743 17410317 17407743 ID=Msa0538240;Name=Msa0538240
chr4_1 mRNA 17407743 17410317 17407743 ID=Msa0538240-mRNA-1;Parent=Msa0538240;Name=Msa0538240-mRNA-1;_AED=0.38;_eAED=0.38;_QI=0|0.33|0.25|1|1|1|4|15|117
chr4_1 exon 17407743 17407818 17407743 ID=Msa0538240-mRNA-1:exon:5208;Parent=Msa0538240-mRNA-1
chr4_1 exon 17409352 17409390 17409352 ID=Msa0538240-mRNA-1:exon:5207;Parent=Msa0538240-mRNA-1
chr4_1 exon 17409981 17410069 17409981 ID=Msa0538240-mRNA-1:exon:5206;Parent=Msa0538240-mRNA-1
chr4_1 exon 17410153 17410317 17410153 ID=Msa0538240-mRNA-1:exon:5205;Parent=Msa0538240-mRNA-1
chr4_1 CDS 17410153 17410317 17410153 ID=Msa0538240-mRNA-1:cds;Parent=Msa0538240-mRNA-1
chr4_1 CDS 17409981 17410069 17409981 ID=Msa0538240-mRNA-1:cds;Parent=Msa0538240-mRNA-1
chr4_1 CDS 17409352 17409390 17409352 ID=Msa0538240-mRNA-1:cds;Parent=Msa0538240-mRNA-1
chr4_1 CDS 17407758 17407818 17407758 ID=Msa0538240-mRNA-1:cds;Parent=Msa0538240-mRNA-1
chr4_1 three_prime_UTR 17407743 17407757 17407743 ID=Msa0538240-mRNA-1:three_prime_utr;Parent=Msa0538240-mRNA-1
Gene Sequence

>Msa0538240

ATGAAGGTCGTTGCATGTCTCGTTTTGGTGTTGTGCATTGTTGTTGCACCTATTGCAGAAGCTGATAGATTTGCCTTTATTATTTATACTCTTACTCCATGCTATCCTTTTCTTCAAGGTTATATTTCAACTGCTGACCCATATTGTTGTGAAGCAGTGAAGAAAACTTTGAATGTGGAGAATGGTGCTGCCCTATTTGCCTTGTGTGGTATTCAAACACCCTACCAGATTACTCGCGATATCAACTGTACCAAGATTATTGAACGCGATGAAGATGATTATGATGAAGATGAAATCAAGGGTGTGGAAGTTGTGGCGGATGTTGGATCAAGGAATATTGTCACCACTATATAG

Protein sequence

>Msa0538240

MKVVACLVLVLCIVVAPIAEADRFAFIIYTLTPCYPFLQGYISTADPYCCEAVKKTLNVENGAALFALCGIQTPYQITRDINCTKIIERDEDDYDEDEIKGVEVVADVGSRNIVTTI*