AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0100800


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0100800 MtrunA17_Chr1g0148991 98.824 85 1 0 1 85 1 85 7.55e-57 171
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0100800 AT5G25450.3 74.713 87 22 0 1 87 1 87 2.62e-44 138
Msa0100800 AT4G32470.2 76.471 85 20 0 1 85 1 85 2.92e-44 139
Msa0100800 AT4G32470.1 74.725 91 22 1 1 90 1 91 4.15e-44 139
Msa0100800 AT5G25450.2 76.471 85 20 0 1 85 1 85 6.62e-44 138
Msa0100800 AT5G25450.1 73.626 91 23 1 1 90 1 91 2.83e-43 137

Find 16 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTATTACGATTTGGATATTA+AGG 0.274133 1_3:+7209125 Msa0100800:CDS
ACCGTATTTGCGAAGACGTT+TGG 0.293147 1_3:-7208989 None:intergenic
GTATCTTCCTGAGGATCTTC+AGG 0.339636 1_3:+7209233 Msa0100800:CDS
GTATGATCCGTATTACGATT+TGG 0.362212 1_3:+7209116 Msa0100800:CDS
TGAGGATCTTCAGGTTGGTT+TGG 0.364077 1_3:+7209242 Msa0100800:CDS
TCCAAACGTCTTCGCAAATA+CGG 0.376472 1_3:+7208988 Msa0100800:CDS
CGAGCATCAACAACCTCCTT+TGG 0.426514 1_3:-7209165 None:intergenic
AGGAAGATACTCATGCTTCA+TGG 0.469418 1_3:-7209220 None:intergenic
TTAATATCCAAATCGTAATA+CGG 0.475035 1_3:-7209123 None:intergenic
CTTCCTGAGGATCTTCAGGT+TGG 0.486843 1_3:+7209237 Msa0100800:CDS
GGCTTTGAATCGGCTTCCAA+AGG 0.532273 1_3:+7209149 Msa0100800:CDS
ATATTAAGGAGGCTTTGAAT+CGG 0.539685 1_3:+7209139 Msa0100800:CDS
AAACCAACCTGAAGATCCTC+AGG 0.545207 1_3:-7209240 None:intergenic
TTTGAATCGGCTTCCAAAGG+AGG 0.563776 1_3:+7209152 Msa0100800:CDS
TTACGATTTGGATATTAAGG+AGG 0.584001 1_3:+7209128 Msa0100800:CDS
GAAGCATGAGTATCTTCCTG+AGG 0.684541 1_3:+7209224 Msa0100800:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATACAATTTCACAAATTA+GGG - chr1_3:7209062-7209081 None:intergenic 15.0%
!! AAAAAACGAAATGAAGATTT+AGG - chr1_3:7209027-7209046 None:intergenic 20.0%
!! CAAATACAATTTCACAAATT+AGG - chr1_3:7209063-7209082 None:intergenic 20.0%
!!! TGTATTTGATTTGTGAAATT+AGG + chr1_3:7209075-7209094 Msa0100800:intron 20.0%
!!! GTATTTGATTTGTGAAATTA+GGG + chr1_3:7209076-7209095 Msa0100800:intron 20.0%
!! TTAATATCCAAATCGTAATA+CGG - chr1_3:7209126-7209145 None:intergenic 20.0%
!! GTATTACGATTTGGATATTA+AGG + chr1_3:7209125-7209144 Msa0100800:CDS 25.0%
TTGTAGATCCAAAGAAAAAC+TGG + chr1_3:7208938-7208957 Msa0100800:CDS 30.0%
! TTACGATTTGGATATTAAGG+AGG + chr1_3:7209128-7209147 Msa0100800:CDS 30.0%
!! ATATTAAGGAGGCTTTGAAT+CGG + chr1_3:7209139-7209158 Msa0100800:CDS 30.0%
GTATGATCCGTATTACGATT+TGG + chr1_3:7209116-7209135 Msa0100800:CDS 35.0%
TCCAAACGTCTTCGCAAATA+CGG + chr1_3:7208988-7209007 Msa0100800:CDS 40.0%
AGGAAGATACTCATGCTTCA+TGG - chr1_3:7209223-7209242 None:intergenic 40.0%
! GCAGCGAACCAGTTTTTCTT+TGG - chr1_3:7208949-7208968 None:intergenic 45.0%
ACCGTATTTGCGAAGACGTT+TGG - chr1_3:7208992-7209011 None:intergenic 45.0%
! TTTGAATCGGCTTCCAAAGG+AGG + chr1_3:7209152-7209171 Msa0100800:CDS 45.0%
GAAGCATGAGTATCTTCCTG+AGG + chr1_3:7209224-7209243 Msa0100800:CDS 45.0%
GTATCTTCCTGAGGATCTTC+AGG + chr1_3:7209233-7209252 Msa0100800:CDS 45.0%
AAACCAACCTGAAGATCCTC+AGG - chr1_3:7209243-7209262 None:intergenic 45.0%
!! TGAGGATCTTCAGGTTGGTT+TGG + chr1_3:7209242-7209261 Msa0100800:CDS 45.0%
!! GGCTTTGAATCGGCTTCCAA+AGG + chr1_3:7209149-7209168 Msa0100800:CDS 50.0%
CGAGCATCAACAACCTCCTT+TGG - chr1_3:7209168-7209187 None:intergenic 50.0%
CTTCCTGAGGATCTTCAGGT+TGG + chr1_3:7209237-7209256 Msa0100800:CDS 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 7208916 7209275 7208916 ID=Msa0100800;Name=Msa0100800
chr1_3 mRNA 7208916 7209275 7208916 ID=Msa0100800-mRNA-1;Parent=Msa0100800;Name=Msa0100800-mRNA-1;_AED=0.16;_eAED=0.16;_QI=0|0|0|1|1|1|2|0|90
chr1_3 exon 7208916 7209009 7208916 ID=Msa0100800-mRNA-1:exon:2827;Parent=Msa0100800-mRNA-1
chr1_3 exon 7209097 7209275 7209097 ID=Msa0100800-mRNA-1:exon:2828;Parent=Msa0100800-mRNA-1
chr1_3 CDS 7208916 7209009 7208916 ID=Msa0100800-mRNA-1:cds;Parent=Msa0100800-mRNA-1
chr1_3 CDS 7209097 7209275 7209097 ID=Msa0100800-mRNA-1:cds;Parent=Msa0100800-mRNA-1
Gene Sequence

>Msa0100800

ATGGCGTCTTTGCTACAAGCGATTGTAGATCCAAAGAAAAACTGGTTCGCTGCTCAACACATGAAAGCTGTTTCCAAACGTCTTCGCAAATACGGGTTACGATATGATGATCTGTATGATCCGTATTACGATTTGGATATTAAGGAGGCTTTGAATCGGCTTCCAAAGGAGGTTGTTGATGCTCGTCATGCTCGTCTTAAGCGTGCTATTGATCTTTCCATGAAGCATGAGTATCTTCCTGAGGATCTTCAGGTTGGTTTGGTTTTTCGTTAA

Protein sequence

>Msa0100800

MASLLQAIVDPKKNWFAAQHMKAVSKRLRKYGLRYDDLYDPYYDLDIKEALNRLPKEVVDARHARLKRAIDLSMKHEYLPEDLQVGLVFR*