AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0317510


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0317510 MtrunA17_Chr2g0290831 91.781 73 6 0 1 73 1 73 7.12e-43 133
Msa0317510 MtrunA17_Chr3g0120541 47.887 71 37 0 2 72 3 73 6.99e-18 71.2
Msa0317510 MtrunA17_Chr6g0483521 54.286 70 32 0 1 70 1 70 1.33e-17 73.2
Msa0317510 MtrunA17_Chr6g0483581 49.315 73 37 0 1 73 1 73 1.40e-16 70.5
Msa0317510 MtrunA17_Chr3g0120551 47.143 70 37 0 2 71 3 72 1.46e-16 68.2
Msa0317510 MtrunA17_Chr6g0483511 51.429 70 34 0 1 70 1 70 2.82e-16 68.9
Msa0317510 MtrunA17_Chr6g0483561 49.296 71 36 0 1 71 1 71 2.73e-15 67.0
Msa0317510 MtrunA17_Chr3g0120531 47.222 72 37 1 2 72 3 74 4.19e-15 64.3
Msa0317510 MtrunA17_Chr5g0445581 38.462 65 40 0 1 65 1 65 1.06e-11 54.7
Msa0317510 MtrunA17_Chr5g0438551 45.714 70 37 1 3 71 2 71 1.30e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0317510 AT4G05030.2 58.904 73 30 0 1 73 1 73 9.67e-24 85.5
Msa0317510 AT4G05030.1 60.563 71 28 0 3 73 36 106 4.66e-23 84.7
Msa0317510 AT3G20180.2 43.836 73 41 0 1 73 20 92 2.09e-15 65.9
Msa0317510 AT3G20180.3 41.096 73 43 0 1 73 1 73 1.08e-14 63.5
Msa0317510 AT3G20180.4 41.429 70 41 0 4 73 2 71 1.97e-13 60.5
Msa0317510 AT3G20180.1 41.791 67 39 0 7 73 3 69 3.77e-13 59.7
Msa0317510 AT3G07600.1 41.667 72 42 0 1 72 1 72 7.38e-12 57.4

Find 10 sgRNAs with CRISPR-Local

Find 18 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGACAAGATAGTAGTTAT+TGG 0.241019 2_4:-15397696 Msa0317510:CDS
AGCTACAACCTTGAGTGCCT+TGG 0.451895 2_4:+15398002 None:intergenic
CAAACTGAAATTGTCAGCTT+AGG 0.480321 2_4:-15397621 Msa0317510:CDS
AAGGCACTCAAGGTTGTAGC+TGG 0.487303 2_4:-15398000 Msa0317510:CDS
AAGATAGTAGTTATTGGAGA+TGG 0.521542 2_4:-15397690 Msa0317510:CDS
GCAGCAAAAGATTGTGATGA+GGG 0.535212 2_4:-15398052 Msa0317510:CDS
GTGTCGCACCAAGGCACTCA+AGG 0.539664 2_4:-15398010 Msa0317510:CDS
AAGGTTGTAGCTGGAGCAAA+CGG 0.547469 2_4:-15397991 Msa0317510:intron
TGCAGCAAAAGATTGTGATG+AGG 0.660386 2_4:-15398053 Msa0317510:CDS
ATGTCAAAAGTGTCGCACCA+AGG 0.695558 2_4:-15398019 Msa0317510:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTACTAAAATTTTGTGATT+TGG - chr2_4:15397911-15397930 Msa0317510:intron 20.0%
!! AATTGTTTGAGAAAAAAAGT+TGG - chr2_4:15398026-15398045 Msa0317510:CDS 20.0%
! TTAACGATTGAAATTAGTGA+CGG - chr2_4:15397776-15397795 Msa0317510:intron 25.0%
! AAAGACAAGATAGTAGTTAT+TGG - chr2_4:15397975-15397994 Msa0317510:intron 25.0%
AAGATAGTAGTTATTGGAGA+TGG - chr2_4:15397981-15398000 Msa0317510:intron 30.0%
!! TTTTGTGATTTGGCAAATGC+AGG - chr2_4:15397921-15397940 Msa0317510:intron 35.0%
! AAATGCAGGTGTGAATTTTG+TGG - chr2_4:15397935-15397954 Msa0317510:intron 35.0%
! AATGCAGGTGTGAATTTTGT+GGG - chr2_4:15397936-15397955 Msa0317510:intron 35.0%
! TGTGAATTTTGTGGGATTAG+AGG - chr2_4:15397944-15397963 Msa0317510:intron 35.0%
! GTGAATTTTGTGGGATTAGA+GGG - chr2_4:15397945-15397964 Msa0317510:intron 35.0%
CAAACTGAAATTGTCAGCTT+AGG - chr2_4:15398050-15398069 Msa0317510:CDS 35.0%
TGCAGCAAAAGATTGTGATG+AGG - chr2_4:15397618-15397637 Msa0317510:CDS 40.0%
GCAGCAAAAGATTGTGATGA+GGG - chr2_4:15397619-15397638 Msa0317510:CDS 40.0%
!! ATGTCAAAAGTGTCGCACCA+AGG - chr2_4:15397652-15397671 Msa0317510:CDS 45.0%
AAGGTTGTAGCTGGAGCAAA+CGG - chr2_4:15397680-15397699 Msa0317510:CDS 45.0%
AGCTACAACCTTGAGTGCCT+TGG + chr2_4:15397672-15397691 None:intergenic 50.0%
! AAGGCACTCAAGGTTGTAGC+TGG - chr2_4:15397671-15397690 Msa0317510:CDS 50.0%
! GTGTCGCACCAAGGCACTCA+AGG - chr2_4:15397661-15397680 Msa0317510:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 15397617 15398076 15397617 ID=Msa0317510;Name=Msa0317510
chr2_4 mRNA 15397617 15398076 15397617 ID=Msa0317510-mRNA-1;Parent=Msa0317510;Name=Msa0317510-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|1|1|0.5|2|0|73
chr2_4 exon 15397992 15398076 15397992 ID=Msa0317510-mRNA-1:exon:5747;Parent=Msa0317510-mRNA-1
chr2_4 exon 15397617 15397750 15397617 ID=Msa0317510-mRNA-1:exon:5746;Parent=Msa0317510-mRNA-1
chr2_4 CDS 15397992 15398076 15397992 ID=Msa0317510-mRNA-1:cds;Parent=Msa0317510-mRNA-1
chr2_4 CDS 15397617 15397750 15397617 ID=Msa0317510-mRNA-1:cds;Parent=Msa0317510-mRNA-1
Gene Sequence

>Msa0317510

TTGCAGCAAAAGATTGTGATGAGGGTTAGCATGAGATGTCAAAAGTGTCGCACCAAGGCACTCAAGGTTGTAGCTGGAGCAAACGGTGTGAATTTTGTGGGATTAGAGGGAGATGAGAAAGACAAGATAGTAGTTATTGGAGATGGTGTAGATGCTGTCAAGTTGACAAATTGTTTGAGAAAAAAAGTTGGACAAACTGAAATTGTCAGCTTAGGAGAA

Protein sequence

>Msa0317510

LQQKIVMRVSMRCQKCRTKALKVVAGANGVNFVGLEGDEKDKIVVIGDGVDAVKLTNCLRKKVGQTEIVSLGE