AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1160690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1160690 MtrunA17_Chr7g0256121 95.349 43 2 0 1 43 352 394 3.79e-23 88.6
Msa1160690 MtrunA17_Chr3g0094081 59.524 42 17 0 2 43 334 375 6.50e-13 60.1
Msa1160690 MtrunA17_Chr5g0441461 58.974 39 16 0 2 40 358 396 5.91e-12 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1160690 AT2G26850.1 60.465 43 17 0 1 43 329 371 9.03e-14 62.8
Msa1160690 AT2G41170.1 55.814 43 19 0 1 43 329 371 2.88e-12 58.5
Msa1160690 AT2G41170.2 55.814 43 19 0 1 43 362 404 2.89e-12 58.5

Find 27 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAATAAGGAGAAGAAATA+AGG 0.280654 7_4:+50744359 Msa1160690:five_prime_UTR
ATGTGAATGTAAAGGCTTAA+AGG 0.285660 7_4:+50745099 Msa1160690:three_prime_UTR
GGTGACAGATACAGTGATTT+TGG 0.287163 7_4:+50744851 Msa1160690:intron
GAACAAGGAAATGAAATAAA+AGG 0.299495 7_4:+50744939 Msa1160690:CDS
AATTCAGTGGAGAAGAAATA+AGG 0.338860 7_4:+50744346 Msa1160690:five_prime_UTR
TCAAGTTTAGACCTATAGTT+AGG 0.348513 7_4:-50745155 None:intergenic
GTATAGTGTCATTGGTCATT+TGG 0.367045 7_4:+50744689 Msa1160690:five_prime_UTR
CATTGCCAATGTCACAATAA+AGG 0.376211 7_4:+50744735 Msa1160690:five_prime_UTR
TGCTTAGATGACTTAAAGCC+TGG 0.448701 7_4:+50744311 Msa1160690:five_prime_UTR
TTACAAAGTGGAAGAAACTT+TGG 0.456123 7_4:+50745003 Msa1160690:CDS
GGTTGGTGGTATAGTGTCAT+TGG 0.469917 7_4:+50744681 Msa1160690:intron
TCTTACCTTTATTGTGACAT+TGG 0.477470 7_4:-50744740 None:intergenic
TGAATTTCAACATGATCTCC+AGG 0.484749 7_4:-50744329 None:intergenic
CTTTATTGTGACATTGGCAA+TGG 0.507841 7_4:-50744734 None:intergenic
CTAAACTTGAAAATTTACAT+TGG 0.512613 7_4:+50745168 Msa1160690:three_prime_UTR
TTGGAAACATGTCAAGGTGA+TGG 0.516906 7_4:+50744708 Msa1160690:five_prime_UTR
TTCCTAAAATGTGAATGTAA+AGG 0.517982 7_4:+50745091 Msa1160690:three_prime_UTR
TGTCACTCATTCCTAACTAT+AGG 0.520822 7_4:+50745144 Msa1160690:three_prime_UTR
TGGAAACATGTCAAGGTGAT+GGG 0.523680 7_4:+50744709 Msa1160690:five_prime_UTR
GAGTTCACACAATACACAGC+TGG 0.557018 7_4:+50744873 Msa1160690:five_prime_UTR
AATACACAGCTGGCTCAAGA+TGG 0.566869 7_4:+50744883 Msa1160690:five_prime_UTR
GAGATCATGTTGAAATTCAG+TGG 0.569671 7_4:+50744333 Msa1160690:five_prime_UTR
GTACACTATTGCTTATGTAG+TGG 0.615007 7_4:-50745221 None:intergenic
GGTCATTTGGAAACATGTCA+AGG 0.617542 7_4:+50744702 Msa1160690:five_prime_UTR
AATCAGAAAGTTGCATAGCA+AGG 0.622859 7_4:+50744974 Msa1160690:CDS
GCATACAAGACAATGCTAAG+TGG 0.630540 7_4:+50745334 Msa1160690:three_prime_UTR
GCAAGGAAGAGATTACAAAG+TGG 0.674384 7_4:+50744991 Msa1160690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAGTTAATATTCT+AGG - chr7_4:50744487-50744506 None:intergenic 10.0%
!!! TTTTAAAAATGTTTTGTTAT+AGG + chr7_4:50744660-50744679 Msa1160690:intron 10.0%
!! AAAAAAAAAGTTAATATTCT+AGG - chr7_4:50744487-50744506 None:intergenic 10.0%
!!! TTTTAAAAATGTTTTGTTAT+AGG + chr7_4:50744660-50744679 Msa1160690:intron 10.0%
!!! TAACTTTTTTTTTTTTGAAG+AGG + chr7_4:50744494-50744513 Msa1160690:intron 15.0%
!!! AACTTTTTTTTTTTTGAAGA+GGG + chr7_4:50744495-50744514 Msa1160690:intron 15.0%
!!! TTGATAATAGTTAATATTCT+AGG - chr7_4:50744522-50744541 None:intergenic 15.0%
!! TACAATGAAACATAATTTAA+GGG - chr7_4:50744805-50744824 None:intergenic 15.0%
!! ATACAATGAAACATAATTTA+AGG - chr7_4:50744806-50744825 None:intergenic 15.0%
!!! TAACTTTTTTTTTTTTGAAG+AGG + chr7_4:50744494-50744513 Msa1160690:intron 15.0%
!!! AACTTTTTTTTTTTTGAAGA+GGG + chr7_4:50744495-50744514 Msa1160690:intron 15.0%
!!! TTGATAATAGTTAATATTCT+AGG - chr7_4:50744522-50744541 None:intergenic 15.0%
!! TACAATGAAACATAATTTAA+GGG - chr7_4:50744805-50744824 None:intergenic 15.0%
!! ATACAATGAAACATAATTTA+AGG - chr7_4:50744806-50744825 None:intergenic 15.0%
!!! AAAAATGTTTTGTTATAGGT+TGG + chr7_4:50744664-50744683 Msa1160690:intron 20.0%
!! ACAATGAAACATAATTTAAG+GGG - chr7_4:50744804-50744823 None:intergenic 20.0%
!! GATGATTAAATCAATAATGT+TGG + chr7_4:50744830-50744849 Msa1160690:intron 20.0%
!!! TGAAATAAAAGGTTTTTATG+CGG + chr7_4:50744950-50744969 Msa1160690:CDS 20.0%
!! CTAAACTTGAAAATTTACAT+TGG + chr7_4:50745168-50745187 Msa1160690:three_prime_UTR 20.0%
!!! AAAAATGTTTTGTTATAGGT+TGG + chr7_4:50744664-50744683 Msa1160690:intron 20.0%
!! ACAATGAAACATAATTTAAG+GGG - chr7_4:50744804-50744823 None:intergenic 20.0%
!! GATGATTAAATCAATAATGT+TGG + chr7_4:50744830-50744849 Msa1160690:intron 20.0%
!!! TGAAATAAAAGGTTTTTATG+CGG + chr7_4:50744950-50744969 Msa1160690:CDS 20.0%
!! CTAAACTTGAAAATTTACAT+TGG + chr7_4:50745168-50745187 Msa1160690:three_prime_UTR 20.0%
! AGAAATAAGGAGAAGAAATA+AGG + chr7_4:50744359-50744378 Msa1160690:five_prime_UTR 25.0%
! TATCAATGTTTGTGATACAT+TGG + chr7_4:50744536-50744555 Msa1160690:intron 25.0%
! AATGAAACATAATTTAAGGG+GGG - chr7_4:50744802-50744821 None:intergenic 25.0%
! CAATGAAACATAATTTAAGG+GGG - chr7_4:50744803-50744822 None:intergenic 25.0%
! AGAAAAAATCATAGAGAACA+AGG + chr7_4:50744924-50744943 Msa1160690:CDS 25.0%
! GAACAAGGAAATGAAATAAA+AGG + chr7_4:50744939-50744958 Msa1160690:CDS 25.0%
!! GAAATAAAAGGTTTTTATGC+GGG + chr7_4:50744951-50744970 Msa1160690:CDS 25.0%
!!! TGCTATTCAACATTTTTTGT+TGG - chr7_4:50745029-50745048 None:intergenic 25.0%
! TTCCTAAAATGTGAATGTAA+AGG + chr7_4:50745091-50745110 Msa1160690:three_prime_UTR 25.0%
! AGAAATAAGGAGAAGAAATA+AGG + chr7_4:50744359-50744378 Msa1160690:five_prime_UTR 25.0%
! TATCAATGTTTGTGATACAT+TGG + chr7_4:50744536-50744555 Msa1160690:intron 25.0%
! AATGAAACATAATTTAAGGG+GGG - chr7_4:50744802-50744821 None:intergenic 25.0%
! CAATGAAACATAATTTAAGG+GGG - chr7_4:50744803-50744822 None:intergenic 25.0%
! AGAAAAAATCATAGAGAACA+AGG + chr7_4:50744924-50744943 Msa1160690:CDS 25.0%
! GAACAAGGAAATGAAATAAA+AGG + chr7_4:50744939-50744958 Msa1160690:CDS 25.0%
!! GAAATAAAAGGTTTTTATGC+GGG + chr7_4:50744951-50744970 Msa1160690:CDS 25.0%
!!! TGCTATTCAACATTTTTTGT+TGG - chr7_4:50745029-50745048 None:intergenic 25.0%
! TTCCTAAAATGTGAATGTAA+AGG + chr7_4:50745091-50745110 Msa1160690:three_prime_UTR 25.0%
AATTCAGTGGAGAAGAAATA+AGG + chr7_4:50744346-50744365 Msa1160690:five_prime_UTR 30.0%
TTTATGCGACTATTTAGAAG+AGG - chr7_4:50744425-50744444 None:intergenic 30.0%
TGTAGTCGATAAACAAAAGT+TGG + chr7_4:50744451-50744470 Msa1160690:intron 30.0%
GTTAATATTCTAGGTCTGTT+AGG - chr7_4:50744478-50744497 None:intergenic 30.0%
!! AATGTTTTGTTATAGGTTGG+TGG + chr7_4:50744667-50744686 Msa1160690:intron 30.0%
TCTTACCTTTATTGTGACAT+TGG - chr7_4:50744743-50744762 None:intergenic 30.0%
AGAAGAATTAAAATGCATGC+TGG - chr7_4:50744773-50744792 None:intergenic 30.0%
TTACAAAGTGGAAGAAACTT+TGG + chr7_4:50745003-50745022 Msa1160690:CDS 30.0%
! AGCCTTTACATTCACATTTT+AGG - chr7_4:50745096-50745115 None:intergenic 30.0%
ATGTGAATGTAAAGGCTTAA+AGG + chr7_4:50745099-50745118 Msa1160690:three_prime_UTR 30.0%
TCAAGTTTAGACCTATAGTT+AGG - chr7_4:50745158-50745177 None:intergenic 30.0%
AATTCAGTGGAGAAGAAATA+AGG + chr7_4:50744346-50744365 Msa1160690:five_prime_UTR 30.0%
TTTATGCGACTATTTAGAAG+AGG - chr7_4:50744425-50744444 None:intergenic 30.0%
TGTAGTCGATAAACAAAAGT+TGG + chr7_4:50744451-50744470 Msa1160690:intron 30.0%
GTTAATATTCTAGGTCTGTT+AGG - chr7_4:50744478-50744497 None:intergenic 30.0%
!! AATGTTTTGTTATAGGTTGG+TGG + chr7_4:50744667-50744686 Msa1160690:intron 30.0%
TCTTACCTTTATTGTGACAT+TGG - chr7_4:50744743-50744762 None:intergenic 30.0%
AGAAGAATTAAAATGCATGC+TGG - chr7_4:50744773-50744792 None:intergenic 30.0%
TTACAAAGTGGAAGAAACTT+TGG + chr7_4:50745003-50745022 Msa1160690:CDS 30.0%
! AGCCTTTACATTCACATTTT+AGG - chr7_4:50745096-50745115 None:intergenic 30.0%
ATGTGAATGTAAAGGCTTAA+AGG + chr7_4:50745099-50745118 Msa1160690:three_prime_UTR 30.0%
TCAAGTTTAGACCTATAGTT+AGG - chr7_4:50745158-50745177 None:intergenic 30.0%
TGAATTTCAACATGATCTCC+AGG - chr7_4:50744332-50744351 None:intergenic 35.0%
GAGATCATGTTGAAATTCAG+TGG + chr7_4:50744333-50744352 Msa1160690:five_prime_UTR 35.0%
! GTATAGTGTCATTGGTCATT+TGG + chr7_4:50744689-50744708 Msa1160690:five_prime_UTR 35.0%
CTTTATTGTGACATTGGCAA+TGG - chr7_4:50744737-50744756 None:intergenic 35.0%
CATTGCCAATGTCACAATAA+AGG + chr7_4:50744735-50744754 Msa1160690:five_prime_UTR 35.0%
AGAATTAAAATGCATGCTGG+TGG - chr7_4:50744770-50744789 None:intergenic 35.0%
AATCAGAAAGTTGCATAGCA+AGG + chr7_4:50744974-50744993 Msa1160690:CDS 35.0%
TGTCACTCATTCCTAACTAT+AGG + chr7_4:50745144-50745163 Msa1160690:three_prime_UTR 35.0%
GTACACTATTGCTTATGTAG+TGG - chr7_4:50745224-50745243 None:intergenic 35.0%
TGAATTTCAACATGATCTCC+AGG - chr7_4:50744332-50744351 None:intergenic 35.0%
GAGATCATGTTGAAATTCAG+TGG + chr7_4:50744333-50744352 Msa1160690:five_prime_UTR 35.0%
! GTATAGTGTCATTGGTCATT+TGG + chr7_4:50744689-50744708 Msa1160690:five_prime_UTR 35.0%
CTTTATTGTGACATTGGCAA+TGG - chr7_4:50744737-50744756 None:intergenic 35.0%
CATTGCCAATGTCACAATAA+AGG + chr7_4:50744735-50744754 Msa1160690:five_prime_UTR 35.0%
AGAATTAAAATGCATGCTGG+TGG - chr7_4:50744770-50744789 None:intergenic 35.0%
AATCAGAAAGTTGCATAGCA+AGG + chr7_4:50744974-50744993 Msa1160690:CDS 35.0%
TGTCACTCATTCCTAACTAT+AGG + chr7_4:50745144-50745163 Msa1160690:three_prime_UTR 35.0%
GTACACTATTGCTTATGTAG+TGG - chr7_4:50745224-50745243 None:intergenic 35.0%
TGCTTAGATGACTTAAAGCC+TGG + chr7_4:50744311-50744330 Msa1160690:five_prime_UTR 40.0%
GGTCATTTGGAAACATGTCA+AGG + chr7_4:50744702-50744721 Msa1160690:five_prime_UTR 40.0%
TTGGAAACATGTCAAGGTGA+TGG + chr7_4:50744708-50744727 Msa1160690:five_prime_UTR 40.0%
TGGAAACATGTCAAGGTGAT+GGG + chr7_4:50744709-50744728 Msa1160690:five_prime_UTR 40.0%
! GGTGACAGATACAGTGATTT+TGG + chr7_4:50744851-50744870 Msa1160690:intron 40.0%
GCAAGGAAGAGATTACAAAG+TGG + chr7_4:50744991-50745010 Msa1160690:CDS 40.0%
TGCTTAGATGACTTAAAGCC+TGG + chr7_4:50744311-50744330 Msa1160690:five_prime_UTR 40.0%
GGTCATTTGGAAACATGTCA+AGG + chr7_4:50744702-50744721 Msa1160690:five_prime_UTR 40.0%
TTGGAAACATGTCAAGGTGA+TGG + chr7_4:50744708-50744727 Msa1160690:five_prime_UTR 40.0%
TGGAAACATGTCAAGGTGAT+GGG + chr7_4:50744709-50744728 Msa1160690:five_prime_UTR 40.0%
! GGTGACAGATACAGTGATTT+TGG + chr7_4:50744851-50744870 Msa1160690:intron 40.0%
GCAAGGAAGAGATTACAAAG+TGG + chr7_4:50744991-50745010 Msa1160690:CDS 40.0%
!! GGTTGGTGGTATAGTGTCAT+TGG + chr7_4:50744681-50744700 Msa1160690:intron 45.0%
GAGTTCACACAATACACAGC+TGG + chr7_4:50744873-50744892 Msa1160690:five_prime_UTR 45.0%
! AATACACAGCTGGCTCAAGA+TGG + chr7_4:50744883-50744902 Msa1160690:five_prime_UTR 45.0%
!! GGTTGGTGGTATAGTGTCAT+TGG + chr7_4:50744681-50744700 Msa1160690:intron 45.0%
GAGTTCACACAATACACAGC+TGG + chr7_4:50744873-50744892 Msa1160690:five_prime_UTR 45.0%
! AATACACAGCTGGCTCAAGA+TGG + chr7_4:50744883-50744902 Msa1160690:five_prime_UTR 45.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 50744293 50745354 50744293 ID=Msa1160690;Name=Msa1160690
chr7_4 mRNA 50744293 50745354 50744293 ID=Msa1160690-mRNA-1;Parent=Msa1160690;Name=Msa1160690-mRNA-1;_AED=0.01;_eAED=0.01;_QI=219|1|1|1|0.5|0.66|3|308|43
chr7_4 exon 50744293 50744380 50744293 ID=Msa1160690-mRNA-1:exon:14179;Parent=Msa1160690-mRNA-1
chr7_4 exon 50744682 50744756 50744682 ID=Msa1160690-mRNA-1:exon:14180;Parent=Msa1160690-mRNA-1
chr7_4 exon 50744859 50745354 50744859 ID=Msa1160690-mRNA-1:exon:14181;Parent=Msa1160690-mRNA-1
chr7_4 five_prime_UTR 50744293 50744380 50744293 ID=Msa1160690-mRNA-1:five_prime_utr;Parent=Msa1160690-mRNA-1
chr7_4 five_prime_UTR 50744682 50744756 50744682 ID=Msa1160690-mRNA-1:five_prime_utr;Parent=Msa1160690-mRNA-1
chr7_4 five_prime_UTR 50744859 50744914 50744859 ID=Msa1160690-mRNA-1:five_prime_utr;Parent=Msa1160690-mRNA-1
chr7_4 CDS 50744915 50745046 50744915 ID=Msa1160690-mRNA-1:cds;Parent=Msa1160690-mRNA-1
chr7_4 three_prime_UTR 50745047 50745354 50745047 ID=Msa1160690-mRNA-1:three_prime_utr;Parent=Msa1160690-mRNA-1
Gene Sequence

>Msa1160690

ATGATAAACAGAAAAAATCATAGAGAACAAGGAAATGAAATAAAAGGTTTTTATGCGGGAATCAGAAAGTTGCATAGCAAGGAAGAGATTACAAAGTGGAAGAAACTTTGGCCAACAAAAAATGTTGAATAG

Protein sequence

>Msa1160690

MINRKNHREQGNEIKGFYAGIRKLHSKEEITKWKKLWPTKNVE*