AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0006490

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0006490 MtrunA17_Chr1g0149611 65.714 70 23 1 9 78 440 508 1.02e-22 89.7
Msa0006490 MtrunA17_Chr1g0149581 54.286 70 31 1 9 78 1598 1666 2.88e-17 74.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0006490 AT3G61740.1 48.889 45 23 0 34 78 974 1018 9.39e-11 56.2
Msa0006490 AT3G61740.2 48.889 45 23 0 34 78 938 982 9.66e-11 56.2

Find 23 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTGCAATTTATTGAATTGC+AGG 0.310671 1_1:+9395524 None:intergenic
CTACACCGATTCCAATATTC+CGG 0.336164 1_1:-9395963 Msa0006490:CDS
AAGGAGGAATCCCGGAATAT+TGG 0.345198 1_1:+9395952 None:intergenic
TGCTATTTCAGATGCATTGA+CGG 0.383868 1_1:-9395902 Msa0006490:intron
CCTGCAATTCAATAAATTGC+AGG 0.392271 1_1:-9395524 Msa0006490:CDS
GGAATCGGTGTAGTCAAATT+CGG 0.412765 1_1:+9395973 None:intergenic
ATGAGTGGCGGTGGGGATGA+AGG 0.438746 1_1:+9395933 None:intergenic
CTTCTTCTTCACATTTAAAG+TGG 0.459198 1_1:+9395568 None:intergenic
TTTATTGAATTGCAGGAACA+TGG 0.509510 1_1:+9395531 None:intergenic
GCAAAGAGGGACATATTAGC+TGG 0.519874 1_1:-9395612 Msa0006490:CDS
GGTTATCTTCTTTGCAAAGA+GGG 0.527796 1_1:-9395625 Msa0006490:CDS
TGGGGATGAAGGAGGAATCC+CGG 0.531853 1_1:+9395944 None:intergenic
AGTGGCGGTGGGGATGAAGG+AGG 0.545347 1_1:+9395936 None:intergenic
GAATCCCGGAATATTGGAAT+CGG 0.547638 1_1:+9395958 None:intergenic
TACACCGATTCCAATATTCC+GGG 0.550942 1_1:-9395962 Msa0006490:CDS
AGGTGAATGATGAGTGGCGG+TGG 0.556064 1_1:+9395924 None:intergenic
GTCAATGCATCTGAAATAGC+AGG 0.561079 1_1:+9395904 None:intergenic
GGTGAATGATGAGTGGCGGT+GGG 0.582510 1_1:+9395925 None:intergenic
TTATTGAATTGCAGGAACAT+GGG 0.589124 1_1:+9395532 None:intergenic
AGGTTATCTTCTTTGCAAAG+AGG 0.615001 1_1:-9395626 Msa0006490:CDS
GTGAATGATGAGTGGCGGTG+GGG 0.682408 1_1:+9395926 None:intergenic
AGCAGGTGAATGATGAGTGG+CGG 0.714715 1_1:+9395921 None:intergenic
AATAGCAGGTGAATGATGAG+TGG 0.746575 1_1:+9395918 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAACATTTTCAATGATACAA+TGG - chr1_1:9395660-9395679 Msa0006490:intron 20.0%
!! AGGTCATGTCTAATATTTTA+TGG + chr1_1:9395742-9395761 None:intergenic 25.0%
!!! AATTGATCAAGTTTTATCTC+AGG + chr1_1:9395762-9395781 None:intergenic 25.0%
GGAATTGAATAGAAGATGAA+AGG + chr1_1:9395807-9395826 None:intergenic 30.0%
!! CACTTAGTTTTCTCATATGT+CGG + chr1_1:9395828-9395847 None:intergenic 30.0%
AAGAAGATAACCTACAAAAC+CGG + chr1_1:9395855-9395874 None:intergenic 30.0%
CTTCTTCTTCACATTTAAAG+TGG + chr1_1:9395923-9395942 None:intergenic 30.0%
TTATTGAATTGCAGGAACAT+GGG + chr1_1:9395959-9395978 None:intergenic 30.0%
TTTATTGAATTGCAGGAACA+TGG + chr1_1:9395960-9395979 None:intergenic 30.0%
!! TGCTATTTCAGATGCATTGA+CGG - chr1_1:9395586-9395605 Msa0006490:CDS 35.0%
TGAGAAAACTAAGTGTCAAC+CGG - chr1_1:9395833-9395852 Msa0006490:intron 35.0%
AGGTTATCTTCTTTGCAAAG+AGG - chr1_1:9395862-9395881 Msa0006490:intron 35.0%
GGTTATCTTCTTTGCAAAGA+GGG - chr1_1:9395863-9395882 Msa0006490:intron 35.0%
CCTGCAATTTATTGAATTGC+AGG + chr1_1:9395967-9395986 None:intergenic 35.0%
CCTGCAATTCAATAAATTGC+AGG - chr1_1:9395964-9395983 Msa0006490:CDS 35.0%
GGAATCGGTGTAGTCAAATT+CGG + chr1_1:9395518-9395537 None:intergenic 40.0%
!! CTACACCGATTCCAATATTC+CGG - chr1_1:9395525-9395544 Msa0006490:CDS 40.0%
!! TACACCGATTCCAATATTCC+GGG - chr1_1:9395526-9395545 Msa0006490:CDS 40.0%
GAATCCCGGAATATTGGAAT+CGG + chr1_1:9395533-9395552 None:intergenic 40.0%
AATAGCAGGTGAATGATGAG+TGG + chr1_1:9395573-9395592 None:intergenic 40.0%
! GTCAATGCATCTGAAATAGC+AGG + chr1_1:9395587-9395606 None:intergenic 40.0%
AAAGGTGAATGCAGAAATGC+AGG + chr1_1:9395789-9395808 None:intergenic 40.0%
!! TAAGTGTCAACCGGTTTTGT+AGG - chr1_1:9395842-9395861 Msa0006490:intron 40.0%
AAGGAGGAATCCCGGAATAT+TGG + chr1_1:9395539-9395558 None:intergenic 45.0%
GCAAAGAGGGACATATTAGC+TGG - chr1_1:9395876-9395895 Msa0006490:intron 45.0%
AGCAGGTGAATGATGAGTGG+CGG + chr1_1:9395570-9395589 None:intergenic 50.0%
TGGGGATGAAGGAGGAATCC+CGG + chr1_1:9395547-9395566 None:intergenic 55.0%
GTGAATGATGAGTGGCGGTG+GGG + chr1_1:9395565-9395584 None:intergenic 55.0%
GGTGAATGATGAGTGGCGGT+GGG + chr1_1:9395566-9395585 None:intergenic 55.0%
AGGTGAATGATGAGTGGCGG+TGG + chr1_1:9395567-9395586 None:intergenic 55.0%
ATGAGTGGCGGTGGGGATGA+AGG + chr1_1:9395558-9395577 None:intergenic 60.0%
AGTGGCGGTGGGGATGAAGG+AGG + chr1_1:9395555-9395574 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 9395509 9396001 9395509 ID=Msa0006490;Name=Msa0006490
chr1_1 mRNA 9395509 9396001 9395509 ID=Msa0006490-mRNA-1;Parent=Msa0006490;Name=Msa0006490-mRNA-1;_AED=0.66;_eAED=0.66;_QI=0|0|0|0.5|0|0|2|0|78
chr1_1 exon 9395903 9396001 9395903 ID=Msa0006490-mRNA-1:exon:3406;Parent=Msa0006490-mRNA-1
chr1_1 exon 9395509 9395646 9395509 ID=Msa0006490-mRNA-1:exon:3405;Parent=Msa0006490-mRNA-1
chr1_1 CDS 9395903 9396001 9395903 ID=Msa0006490-mRNA-1:cds;Parent=Msa0006490-mRNA-1
chr1_1 CDS 9395509 9395646 9395509 ID=Msa0006490-mRNA-1:cds;Parent=Msa0006490-mRNA-1
Gene Sequence

>Msa0006490

ATGAAACCGAATTTGACTACACCGATTCCAATATTCCGGGATTCCTCCTTCATCCCCACCGCCACTCATCATTCACCTGCTATTTCAGATGCATTGACGGTTATCTTCTTTGCAAAGAGGGACATATTAGCTGGTGAAGAAATCACTTATGATTACCACTTTAAATGTGAAGAAGAAGAAGAAAAGAAAATCCCATGTTCCTGCAATTCAATAAATTGCAGGCGCTCTCTAAACTGA
Protein sequence

>Msa0006490

MKPNLTTPIPIFRDSSFIPTATHHSPAISDALTVIFFAKRDILAGEEITYDYHFKCEEEEEKKIPCSCNSINCRRSLN*