AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0677540

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0677540 MtrunA17_Chr2g0281511 83.607 122 20 0 1 122 1 122 1.22e-72 212
Msa0677540 MtrunA17_Chr2g0309121 80.328 122 23 1 1 122 1 121 1.63e-67 199
Msa0677540 MtrunA17_Chr3g0081891 82.500 80 14 0 1 80 1 80 5.13e-43 135
Msa0677540 MtrunA17_Chr7g0276661 34.351 131 66 5 7 119 38 166 6.83e-18 74.7
Msa0677540 MtrunA17_Chr0c01g0489371 41.573 89 50 1 24 110 226 314 2.90e-14 67.4
Msa0677540 MtrunA17_Chr8g0372431 27.835 97 70 0 24 120 6 102 1.62e-13 62.0
Msa0677540 MtrunA17_Chr8g0356961 39.326 89 52 1 24 110 77 165 3.04e-13 62.8
Msa0677540 MtrunA17_Chr8g0356951 39.560 91 51 2 24 110 217 307 4.69e-12 61.2
Msa0677540 MtrunA17_Chr5g0430431 46.296 54 29 0 63 116 201 254 7.33e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATGTTACTGCATCTATTT+TGG 0.128704 4_4:-31603703 Msa0677540:CDS
GAAGTTAATGGTGCTGAATT+AGG 0.163350 4_4:-31603762 Msa0677540:CDS
AAAATTCCGATGTTCGTTAT+TGG 0.193608 4_4:-31603731 Msa0677540:CDS
TACCAGTTTCTTCATTAAAA+AGG 0.201451 4_4:+31603509 None:intergenic
TGTATGCTACCGTCGTTAAC+TGG 0.283121 4_4:-31603342 Msa0677540:CDS
CCTCGACGTGTTGCTGAGAA+TGG 0.340072 4_4:-31603559 Msa0677540:CDS
GAGATTGGAGTTGAAGTTAA+TGG 0.344431 4_4:-31603774 Msa0677540:CDS
CGGTCAATAATCCTCCTAAT+AGG 0.355854 4_4:-31603366 Msa0677540:CDS
TTTGGATGGAAACAATGTTT+TGG 0.356448 4_4:-31603685 Msa0677540:intron
AAGTTAATGGTGCTGAATTA+GGG 0.367629 4_4:-31603761 Msa0677540:CDS
ACGGTAGCATACATCCTATT+AGG 0.440754 4_4:+31603352 None:intergenic
AGCATGCATCATAAATACAT+AGG 0.525952 4_4:-31603451 Msa0677540:CDS
GTATGCTACCGTCGTTAACT+GGG 0.530059 4_4:-31603341 Msa0677540:CDS
CTTGAAAAGTGCCTAAAAGT+TGG 0.570138 4_4:-31603406 Msa0677540:CDS
CATCATAAATACATAGGGAG+AGG 0.571605 4_4:-31603445 Msa0677540:CDS
GCATGCATCATAAATACATA+GGG 0.575971 4_4:-31603450 Msa0677540:CDS
ATAAATACATAGGGAGAGGA+TGG 0.584223 4_4:-31603441 Msa0677540:CDS
GTAGCATACATCCTATTAGG+AGG 0.633251 4_4:+31603355 None:intergenic
ATACTTCCAATAACGAACAT+CGG 0.641741 4_4:+31603725 None:intergenic
CCATTCTCAGCAACACGTCG+AGG 0.662672 4_4:+31603559 None:intergenic
GAATCAATCCCAGTTAACGA+CGG 0.716201 4_4:+31603333 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATGTTACTGCATCTATTT+TGG - chr4_4:31603413-31603432 Msa0677540:CDS 25.0%
! TACCAGTTTCTTCATTAAAA+AGG + chr4_4:31603610-31603629 None:intergenic 25.0%
!! AAATAATGTCACCAACTTTT+AGG + chr4_4:31603724-31603743 None:intergenic 25.0%
! AAGTTAATGGTGCTGAATTA+GGG - chr4_4:31603355-31603374 Msa0677540:CDS 30.0%
AAAATTCCGATGTTCGTTAT+TGG - chr4_4:31603385-31603404 Msa0677540:CDS 30.0%
ATACTTCCAATAACGAACAT+CGG + chr4_4:31603394-31603413 None:intergenic 30.0%
! TTTGGATGGAAACAATGTTT+TGG - chr4_4:31603431-31603450 Msa0677540:CDS 30.0%
! TCATGTTGTTAAGTTGTTGT+TGG - chr4_4:31603487-31603506 Msa0677540:CDS 30.0%
! CTCCTTTTTAATGAAGAAAC+TGG - chr4_4:31603605-31603624 Msa0677540:intron 30.0%
AGCATGCATCATAAATACAT+AGG - chr4_4:31603665-31603684 Msa0677540:intron 30.0%
GCATGCATCATAAATACATA+GGG - chr4_4:31603666-31603685 Msa0677540:intron 30.0%
!! TGGTGACATTATTTTGTTCA+CGG - chr4_4:31603730-31603749 Msa0677540:CDS 30.0%
GAGATTGGAGTTGAAGTTAA+TGG - chr4_4:31603342-31603361 Msa0677540:CDS 35.0%
! GAAGTTAATGGTGCTGAATT+AGG - chr4_4:31603354-31603373 Msa0677540:CDS 35.0%
!! GTTACTGCATCTATTTTGGA+TGG - chr4_4:31603417-31603436 Msa0677540:CDS 35.0%
!!! GGAAACAATGTTTTGGTTAG+TGG - chr4_4:31603438-31603457 Msa0677540:CDS 35.0%
CATCATAAATACATAGGGAG+AGG - chr4_4:31603671-31603690 Msa0677540:intron 35.0%
ATAAATACATAGGGAGAGGA+TGG - chr4_4:31603675-31603694 Msa0677540:intron 35.0%
!! CTTGAAAAGTGCCTAAAAGT+TGG - chr4_4:31603710-31603729 Msa0677540:CDS 35.0%
CGGTCAATAATCCTCCTAAT+AGG - chr4_4:31603750-31603769 Msa0677540:CDS 40.0%
GTAGCATACATCCTATTAGG+AGG + chr4_4:31603764-31603783 None:intergenic 40.0%
ACGGTAGCATACATCCTATT+AGG + chr4_4:31603767-31603786 None:intergenic 40.0%
TGTATGCTACCGTCGTTAAC+TGG - chr4_4:31603774-31603793 Msa0677540:CDS 45.0%
GTATGCTACCGTCGTTAACT+GGG - chr4_4:31603775-31603794 Msa0677540:CDS 45.0%
CCATTCTCAGCAACACGTCG+AGG + chr4_4:31603560-31603579 None:intergenic 55.0%
! CCTCGACGTGTTGCTGAGAA+TGG - chr4_4:31603557-31603576 Msa0677540:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 31603336 31603802 31603336 ID=Msa0677540;Name=Msa0677540
chr4_4 mRNA 31603336 31603802 31603336 ID=Msa0677540-mRNA-1;Parent=Msa0677540;Name=Msa0677540-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|122
chr4_4 exon 31603686 31603802 31603686 ID=Msa0677540-mRNA-1:exon:7831;Parent=Msa0677540-mRNA-1
chr4_4 exon 31603336 31603587 31603336 ID=Msa0677540-mRNA-1:exon:7830;Parent=Msa0677540-mRNA-1
chr4_4 CDS 31603686 31603802 31603686 ID=Msa0677540-mRNA-1:cds;Parent=Msa0677540-mRNA-1
chr4_4 CDS 31603336 31603587 31603336 ID=Msa0677540-mRNA-1:cds;Parent=Msa0677540-mRNA-1
Gene Sequence

>Msa0677540

ATGAATGAGATTGGAGTTGAAGTTAATGGTGCTGAATTAGGGAATCTTCAAAATTCCGATGTTCGTTATTGGAAGTATAATGTTACTGCATCTATTTTGGATGGAAACAATGTTTTGACTTTTCCTCGACGTGTTGCTGAGAATGGTTTGTATATCAATCAATCTAAAATTCTCCTTTTTAATGAAGAAACTGGTAAATCTTATGACTTTGATGTTCACACTGCGTCAAGAAGCATGCATCATAAATACATAGGGAGAGGATGGTACGACTTTGTTCTTGAAAAGTGCCTAAAAGTTGGTGACATTATTTTGTTCACGGTCAATAATCCTCCTAATAGGATGTATGCTACCGTCGTTAACTGGGATTGA
Protein sequence

>Msa0677540

MNEIGVEVNGAELGNLQNSDVRYWKYNVTASILDGNNVLTFPRRVAENGLYINQSKILLFNEETGKSYDFDVHTASRSMHHKYIGRGWYDFVLEKCLKVGDIILFTVNNPPNRMYATVVNWD*