AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1457680

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1457680 MtrunA17_Chr3g0145471 87.778 90 11 0 4 93 1 90 3.36e-42 132
Msa1457680 MtrunA17_Chr4g0038521 47.170 53 27 1 1 52 1 53 5.39e-11 53.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCCACTTGCTCATGGTATT+TGG 0.221621 tig0039078:+17949 Msa1457680:CDS
GATAAGTAGTTGAAAGTTGA+TGG 0.350576 tig0039078:-18037 None:intergenic
TTCTCAGTACAACCACTTCA+AGG 0.423962 tig0039078:+17996 Msa1457680:CDS
ATACCATGAGCAAGTGGAAT+GGG 0.424845 tig0039078:-17945 None:intergenic
AAGCTCAACTTTCACACGCT+TGG 0.439936 tig0039078:+18114 Msa1457680:CDS
TTCATTGGTTCATATTCTAC+CGG 0.459746 tig0039078:+18087 Msa1457680:CDS
TAAAACAAATTAGAATGGAG+TGG 0.483489 tig0039078:+17848 None:intergenic
CTAAGAGAAGGGGTGCAGAA+TGG 0.557799 tig0039078:+17878 Msa1457680:CDS
GTGGGTGCAGTCTAAGAGAA+GGG 0.558450 tig0039078:+17867 Msa1457680:CDS
AAAACAAATTAGAATGGAGT+GGG 0.565648 tig0039078:+17849 None:intergenic
ACCATGAGCAAGTGGAATGG+GGG 0.577759 tig0039078:-17943 None:intergenic
GTGAAAGTTGAGCTTTCCAC+CGG 0.578373 tig0039078:-18106 None:intergenic
AATACCATGAGCAAGTGGAA+TGG 0.583926 tig0039078:-17946 None:intergenic
TGTGTAACTGAGCCTTGAAG+TGG 0.589242 tig0039078:-18008 None:intergenic
ATTGGTTCATATTCTACCGG+TGG 0.591044 tig0039078:+18090 Msa1457680:CDS
GTGCAGAATGGAAACAAGGA+TGG 0.597122 tig0039078:+17890 Msa1457680:CDS
TACCATGAGCAAGTGGAATG+GGG 0.604366 tig0039078:-17944 None:intergenic
AGTGGGTGCAGTCTAAGAGA+AGG 0.606015 tig0039078:+17866 Msa1457680:CDS
TGCCAAATACCATGAGCAAG+TGG 0.608145 tig0039078:-17951 None:intergenic
GAATGGAAACAAGGATGGAG+AGG 0.628361 tig0039078:+17895 Msa1457680:CDS
GCTCATGGTATTTGGCATCG+TGG 0.630406 tig0039078:+17957 Msa1457680:CDS
TGGGTGCAGTCTAAGAGAAG+GGG 0.653177 tig0039078:+17868 Msa1457680:CDS
AGGGGTGCAGAATGGAAACA+AGG 0.663100 tig0039078:+17886 Msa1457680:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGAAAAACATAAGCAAGAA+GGG - tig0039078:18072-18091 None:intergenic 25.0%
! AATGAAAAACATAAGCAAGA+AGG - tig0039078:18073-18092 None:intergenic 25.0%
!! TTCTTGCTTATGTTTTTCAT+TGG + tig0039078:18072-18091 Msa1457680:CDS 25.0%
GATAAGTAGTTGAAAGTTGA+TGG - tig0039078:18040-18059 None:intergenic 30.0%
TGAAAAACATAAGCAAGAAG+GGG - tig0039078:18071-18090 None:intergenic 30.0%
!! TTCATTGGTTCATATTCTAC+CGG + tig0039078:18087-18106 Msa1457680:CDS 30.0%
ATACCATGAGCAAGTGGAAT+GGG - tig0039078:17948-17967 None:intergenic 40.0%
AATACCATGAGCAAGTGGAA+TGG - tig0039078:17949-17968 None:intergenic 40.0%
TTCCACTTGCTCATGGTATT+TGG + tig0039078:17949-17968 Msa1457680:CDS 40.0%
TTCTCAGTACAACCACTTCA+AGG + tig0039078:17996-18015 Msa1457680:CDS 40.0%
! ATTGGTTCATATTCTACCGG+TGG + tig0039078:18090-18109 Msa1457680:CDS 40.0%
GTGCAGAATGGAAACAAGGA+TGG + tig0039078:17890-17909 Msa1457680:CDS 45.0%
GAATGGAAACAAGGATGGAG+AGG + tig0039078:17895-17914 Msa1457680:CDS 45.0%
TACCATGAGCAAGTGGAATG+GGG - tig0039078:17947-17966 None:intergenic 45.0%
TGCCAAATACCATGAGCAAG+TGG - tig0039078:17954-17973 None:intergenic 45.0%
TGTGTAACTGAGCCTTGAAG+TGG - tig0039078:18011-18030 None:intergenic 45.0%
GTGAAAGTTGAGCTTTCCAC+CGG - tig0039078:18109-18128 None:intergenic 45.0%
AAGCTCAACTTTCACACGCT+TGG + tig0039078:18114-18133 Msa1457680:CDS 45.0%
AGTGGGTGCAGTCTAAGAGA+AGG + tig0039078:17866-17885 Msa1457680:CDS 50.0%
GTGGGTGCAGTCTAAGAGAA+GGG + tig0039078:17867-17886 Msa1457680:CDS 50.0%
TGGGTGCAGTCTAAGAGAAG+GGG + tig0039078:17868-17887 Msa1457680:CDS 50.0%
! CTAAGAGAAGGGGTGCAGAA+TGG + tig0039078:17878-17897 Msa1457680:CDS 50.0%
! AGGGGTGCAGAATGGAAACA+AGG + tig0039078:17886-17905 Msa1457680:CDS 50.0%
ACCATGAGCAAGTGGAATGG+GGG - tig0039078:17946-17965 None:intergenic 50.0%
GCTCATGGTATTTGGCATCG+TGG + tig0039078:17957-17976 Msa1457680:CDS 50.0%
ACCCCCATTCCACTTGCTCA+TGG + tig0039078:17942-17961 Msa1457680:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0039078 gene 17862 18143 17862 ID=Msa1457680;Name=Msa1457680
tig0039078 mRNA 17862 18143 17862 ID=Msa1457680-mRNA-1;Parent=Msa1457680;Name=Msa1457680-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|93
tig0039078 exon 17862 18143 17862 ID=Msa1457680-mRNA-1:exon:21323;Parent=Msa1457680-mRNA-1
tig0039078 CDS 17862 18143 17862 ID=Msa1457680-mRNA-1:cds;Parent=Msa1457680-mRNA-1
Gene Sequence

>Msa1457680

ATGGAGTGGGTGCAGTCTAAGAGAAGGGGTGCAGAATGGAAACAAGGATGGAGAGGAAAGAGCATGACTTCTATTTCTGCACCCCCATTCCACTTGCTCATGGTATTTGGCATCGTGGTTAGCTTGTTGTGTTTTTCTCAGTACAACCACTTCAAGGCTCAGTTACACAACACTGCCATCAACTTTCAACTACTTATCTTCTTCTTCCCCTTCTTGCTTATGTTTTTCATTGGTTCATATTCTACCGGTGGAAAGCTCAACTTTCACACGCTTGGAGCATGA
Protein sequence

>Msa1457680

MEWVQSKRRGAEWKQGWRGKSMTSISAPPFHLLMVFGIVVSLLCFSQYNHFKAQLHNTAINFQLLIFFFPFLLMFFIGSYSTGGKLNFHTLGA*