AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0142950


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0142950 MtrunA17_Chr2g0287341 87.952 83 10 0 60 142 118 200 2.09e-46 149
Msa0142950 MtrunA17_Chr2g0286581 40.187 107 51 1 36 142 104 197 6.23e-13 63.2
Msa0142950 MtrunA17_Chr2g0287321 48.000 75 35 2 68 142 107 177 7.02e-13 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTAAGGCAGATCAAATTT+TGG 0.261207 1_4:+1897997 Msa0142950:CDS
TCGGTTTCTGAAAGGGAAAT+TGG 0.276146 1_4:+1898027 Msa0142950:CDS
TTTATCTCAAATGCACATTC+TGG 0.290745 1_4:+1898063 Msa0142950:CDS
AGAGGAAGAAGAGGAGAAGG+AGG 0.456985 1_4:+1897889 Msa0142950:CDS
GTGTCTCAAAAGCTTTCTGC+AGG 0.459684 1_4:+1898099 Msa0142950:CDS
AGAAGAGGAAGAAGAGGAGA+AGG 0.476933 1_4:+1897886 Msa0142950:CDS
AGAGAGACAATTGATGATGA+TGG 0.486004 1_4:+1897970 Msa0142950:CDS
TGGATGTTCGGTTTCTGAAA+GGG 0.496222 1_4:+1898020 Msa0142950:CDS
AGAAGATGATGATGAAGAAG+AGG 0.498596 1_4:+1897871 Msa0142950:CDS
GAAGAAGAAGATGATGAAGA+AGG 0.501500 1_4:+1897758 Msa0142950:CDS
TGATGAAGAAGAGGAAGAAG+AGG 0.506514 1_4:+1897880 Msa0142950:CDS
GTGGATGTTCGGTTTCTGAA+AGG 0.533998 1_4:+1898019 Msa0142950:CDS
GAAGATGATGAAGAAGGAGG+AGG 0.534410 1_4:+1897764 Msa0142950:CDS
AGCTTAGCCAACTCGTTCAT+CGG 0.543217 1_4:-1897923 None:intergenic
AGACAATAATCAATACTAAG+AGG 0.543627 1_4:-1898149 None:intergenic
GATGATGATGGCAGTTGCTA+AGG 0.561376 1_4:+1897982 Msa0142950:CDS
GAAGAAGATGATGAAGAAGG+AGG 0.575374 1_4:+1897761 Msa0142950:CDS
ATCTCAAATGCACATTCTGG+AGG 0.586032 1_4:+1898066 Msa0142950:CDS
ACAATTGCCGATGAACGAGT+TGG 0.627265 1_4:+1897916 Msa0142950:CDS
GATGACGACGATGATGAAGA+TGG 0.645067 1_4:+1897842 Msa0142950:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCAAATTTTGGTGGATGTT+CGG + chr1_4:1898008-1898027 Msa0142950:CDS 30.0%
TTTATCTCAAATGCACATTC+TGG + chr1_4:1898063-1898082 Msa0142950:CDS 30.0%
TCTTCTTCTTCTTCTTCTTG+AGG - chr1_4:1897734-1897753 None:intergenic 35.0%
GAAGAAGAAGATGATGAAGA+AGG + chr1_4:1897758-1897777 Msa0142950:CDS 35.0%
! AGAAGATGATGATGAAGAAG+AGG + chr1_4:1897871-1897890 Msa0142950:CDS 35.0%
!! AGAGAGACAATTGATGATGA+TGG + chr1_4:1897970-1897989 Msa0142950:CDS 35.0%
! TGCTAAGGCAGATCAAATTT+TGG + chr1_4:1897997-1898016 Msa0142950:CDS 35.0%
! TAAGGCAGATCAAATTTTGG+TGG + chr1_4:1898000-1898019 Msa0142950:CDS 35.0%
GAAGAAGATGATGAAGAAGG+AGG + chr1_4:1897761-1897780 Msa0142950:CDS 40.0%
TGATGAAGAAGAGGAAGAAG+AGG + chr1_4:1897880-1897899 Msa0142950:CDS 40.0%
! TGGATGTTCGGTTTCTGAAA+GGG + chr1_4:1898020-1898039 Msa0142950:CDS 40.0%
! TCGGTTTCTGAAAGGGAAAT+TGG + chr1_4:1898027-1898046 Msa0142950:CDS 40.0%
ATCTCAAATGCACATTCTGG+AGG + chr1_4:1898066-1898085 Msa0142950:CDS 40.0%
GAAGATGATGAAGAAGGAGG+AGG + chr1_4:1897764-1897783 Msa0142950:CDS 45.0%
GATGACGACGATGATGAAGA+TGG + chr1_4:1897842-1897861 Msa0142950:CDS 45.0%
AGAAGAGGAAGAAGAGGAGA+AGG + chr1_4:1897886-1897905 Msa0142950:CDS 45.0%
ACAATTGCCGATGAACGAGT+TGG + chr1_4:1897916-1897935 Msa0142950:CDS 45.0%
AGCTTAGCCAACTCGTTCAT+CGG - chr1_4:1897926-1897945 None:intergenic 45.0%
!! GATGATGATGGCAGTTGCTA+AGG + chr1_4:1897982-1898001 Msa0142950:CDS 45.0%
GTGGATGTTCGGTTTCTGAA+AGG + chr1_4:1898019-1898038 Msa0142950:CDS 45.0%
GTGTCTCAAAAGCTTTCTGC+AGG + chr1_4:1898099-1898118 Msa0142950:CDS 45.0%
AGAGGAAGAAGAGGAGAAGG+AGG + chr1_4:1897889-1897908 Msa0142950:CDS 50.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 1897728 1898156 1897728 ID=Msa0142950;Name=Msa0142950
chr1_4 mRNA 1897728 1898156 1897728 ID=Msa0142950-mRNA-1;Parent=Msa0142950;Name=Msa0142950-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|142
chr1_4 exon 1897728 1898156 1897728 ID=Msa0142950-mRNA-1:exon:717;Parent=Msa0142950-mRNA-1
chr1_4 CDS 1897728 1898156 1897728 ID=Msa0142950-mRNA-1:cds;Parent=Msa0142950-mRNA-1
Gene Sequence

>Msa0142950

ATGCCTCAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATGATGAAGAAGGAGGAGGAGATGATGATGATGATGATGATGATGATGAAGCAGAAGTAGCAGATGAAGAAGAAGATGACGACGATGATGAAGATGGTGAAGAAGAAGATGATGATGAAGAAGAGGAAGAAGAGGAGAAGGAGGAGAAACAATTGCCGATGAACGAGTTGGCTAAGCTTGATAATCTTGATGAAGAAGAAAAAGAGAGACAATTGATGATGATGGCAGTTGCTAAGGCAGATCAAATTTTGGTGGATGTTCGGTTTCTGAAAGGGAAATTGGAAACTATTAATGATTTATCTCAAATGCACATTCTGGAGGATAAAATGAAGTGTCTCAAAAGCTTTCTGCAGGTTTATCTCAAGTCAACAACATCTTCATCCTCTTAG

Protein sequence

>Msa0142950

MPQEEEEEEEEEEDDEEGGGDDDDDDDDDEAEVADEEEDDDDDEDGEEEDDDEEEEEEEKEEKQLPMNELAKLDNLDEEEKERQLMMMAVAKADQILVDVRFLKGKLETINDLSQMHILEDKMKCLKSFLQVYLKSTTSSSS*