AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380016544.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016544.01.T01 MTR_3g491820 97.183 71 2 0 13 83 94 164 4.79e-47 147
MsG0380016544.01.T01 MTR_3g491820 97.183 71 2 0 13 83 61 131 4.89e-47 146
MsG0380016544.01.T01 MTR_3g491820 97.183 71 2 0 13 83 31 101 8.84e-47 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380016544.01.T01 AT5G24314 63.415 82 30 0 2 83 80 161 1.50e-33 113
MsG0380016544.01.T01 AT5G24314 63.415 82 30 0 2 83 88 169 1.65e-33 113

Find 19 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGTCTGATCCCTTCAAACC+TGG 0.410327 3:+84969952 MsG0380016542.01.T01:intron
TCAGACTCGGCATACGCCTC+TGG 0.453063 3:-84969937 None:intergenic
ATAATGAGGCCCAGGTTTGA+AGG 0.480274 3:-84969962 None:intergenic
GAGAGCAACATGGATGAGTA+TGG 0.481625 3:+84969850 MsG0380016542.01.T01:CDS
CGCCTCTGGACGGTAAAATC+CGG 0.489373 3:-84969923 None:intergenic
ATTACTCAAAACATGAAGAA+TGG 0.511919 3:-84969887 None:intergenic
TAAAACTCTTTCAAATAATG+AGG 0.525568 3:-84969976 None:intergenic
TCTTTCAAATAATGAGGCCC+AGG 0.542211 3:-84969970 None:intergenic
AGTAATCGAGTGAATGATGC+CGG 0.544993 3:+84969904 MsG0380016542.01.T01:CDS
TGAATGCATAATGGTTATGC+TGG 0.562799 3:+84969560 MsG0380016542.01.T01:intron
TAATGAGGCCCAGGTTTGAA+GGG 0.566321 3:-84969961 None:intergenic
AGTCTGATCCCTTCAAACCT+GGG 0.572137 3:+84969953 MsG0380016542.01.T01:intron
ATGATTCATGCTATTGACAC+AGG 0.580847 3:+84969588 MsG0380016542.01.T01:intron
AGGTTTGAAGGGATCAGACT+CGG 0.605147 3:-84969950 None:intergenic
GTTGCTCTCAACATAAGCGT+TGG 0.607357 3:-84969836 None:intergenic
CGCTTATGTTGAGAGCAACA+TGG 0.607844 3:+84969840 MsG0380016542.01.T01:CDS
TGTGAATGAGATAGCAGCTG+AGG 0.626703 3:+84969813 MsG0380016542.01.T01:intron
ACTCGGCATACGCCTCTGGA+CGG 0.681095 3:-84969933 None:intergenic
AGCAACATGGATGAGTATGG+AGG 0.751548 3:+84969853 MsG0380016542.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAACTCTTTCAAATAATG+AGG - Chr3:84969979-84969998 None:intergenic 20.0%
! ATTACTCAAAACATGAAGAA+TGG - Chr3:84969890-84969909 None:intergenic 25.0%
!! CTTAAATATTCAAGTTCATC+GGG - Chr3:84969631-84969650 None:intergenic 25.0%
!! GCTTAAATATTCAAGTTCAT+CGG - Chr3:84969632-84969651 None:intergenic 25.0%
! CATTTTGCTGCAGATAAAAA+AGG + Chr3:84969659-84969678 MsG0380016542.01.T01:exon 30.0%
ATGATTCATGCTATTGACAC+AGG + Chr3:84969588-84969607 MsG0380016542.01.T01:intron 35.0%
ACTCTTGCAATTGGACATAG+AGG + Chr3:84969758-84969777 MsG0380016542.01.T01:intron 40.0%
AGTAATCGAGTGAATGATGC+CGG + Chr3:84969904-84969923 MsG0380016542.01.T01:CDS 40.0%
GTGAGGAAGATAAAGGATGA+GGG + Chr3:84969732-84969751 MsG0380016542.01.T01:intron 40.0%
TCTTTCAAATAATGAGGCCC+AGG - Chr3:84969973-84969992 None:intergenic 40.0%
TGAGGGAAAACTCTTGCAAT+TGG + Chr3:84969749-84969768 MsG0380016542.01.T01:intron 40.0%
TGATTCTCTGCCCTACAAAA+TGG + Chr3:84969683-84969702 MsG0380016542.01.T01:exon 40.0%
AGCAACATGGATGAGTATGG+AGG + Chr3:84969853-84969872 MsG0380016542.01.T01:CDS 45.0%
AGGTTTGAAGGGATCAGACT+CGG - Chr3:84969953-84969972 None:intergenic 45.0%
AGTCTGATCCCTTCAAACCT+GGG + Chr3:84969953-84969972 MsG0380016542.01.T01:intron 45.0%
ATAATGAGGCCCAGGTTTGA+AGG - Chr3:84969965-84969984 None:intergenic 45.0%
CGCTTATGTTGAGAGCAACA+TGG + Chr3:84969840-84969859 MsG0380016542.01.T01:CDS 45.0%
GAGAGCAACATGGATGAGTA+TGG + Chr3:84969850-84969869 MsG0380016542.01.T01:CDS 45.0%
GGTGAGGAAGATAAAGGATG+AGG + Chr3:84969731-84969750 MsG0380016542.01.T01:intron 45.0%
GTTGCTCTCAACATAAGCGT+TGG - Chr3:84969839-84969858 None:intergenic 45.0%
TAATGAGGCCCAGGTTTGAA+GGG - Chr3:84969964-84969983 None:intergenic 45.0%
TGTGAATGAGATAGCAGCTG+AGG + Chr3:84969813-84969832 MsG0380016542.01.T01:intron 45.0%
! AGGAATGCGCTCCATTTTGT+AGG - Chr3:84969697-84969716 None:intergenic 45.0%
! CACAGGTTTTCACGAGTATC+AGG + Chr3:84969605-84969624 MsG0380016542.01.T01:intron 45.0%
! GGAATGCGCTCCATTTTGTA+GGG - Chr3:84969696-84969715 None:intergenic 45.0%
GAGTCTGATCCCTTCAAACC+TGG + Chr3:84969952-84969971 MsG0380016542.01.T01:intron 50.0%
GGAGCAGGTGAGGAAGATAA+AGG + Chr3:84969725-84969744 MsG0380016542.01.T01:intron 50.0%
! CATTCCTTTTCTCGAGGAGC+AGG + Chr3:84969710-84969729 MsG0380016542.01.T01:CDS 50.0%
CGCCTCTGGACGGTAAAATC+CGG - Chr3:84969926-84969945 None:intergenic 55.0%
CTCACCTGCTCCTCGAGAAA+AGG - Chr3:84969717-84969736 None:intergenic 55.0%
! CTTTTCTCGAGGAGCAGGTG+AGG + Chr3:84969715-84969734 MsG0380016542.01.T01:intron 55.0%
! GGAGCGCATTCCTTTTCTCG+AGG + Chr3:84969704-84969723 MsG0380016542.01.T01:CDS 55.0%
! TGCCGGATTTTACCGTCCAG+AGG + Chr3:84969921-84969940 MsG0380016542.01.T01:CDS 55.0%
ACTCGGCATACGCCTCTGGA+CGG - Chr3:84969936-84969955 None:intergenic 60.0%
TCAGACTCGGCATACGCCTC+TGG - Chr3:84969940-84969959 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
Chr3 gene 84969570 84970005 84969570 ID=MsG0380016544.01;Name=MsG0380016544.01
Chr3 mRNA 84969570 84970005 84969570 ID=MsG0380016544.01.T01;Parent=MsG0380016544.01;Name=MsG0380016544.01.T01;_AED=0.48;_eAED=0.57;_QI=0|0|0|1|1|1|2|0|83
Chr3 exon 84969570 84969609 84969570 ID=MsG0380016544.01.T01:exon:14371;Parent=MsG0380016544.01.T01
Chr3 exon 84969794 84970005 84969794 ID=MsG0380016544.01.T01:exon:14372;Parent=MsG0380016544.01.T01
Chr3 CDS 84969570 84969609 84969570 ID=MsG0380016544.01.T01:cds;Parent=MsG0380016544.01.T01
Chr3 CDS 84969794 84970005 84969794 ID=MsG0380016544.01.T01:cds;Parent=MsG0380016544.01.T01
Gene Sequence

>MsG0380016544.01.T01

ATGGTTATGCTGGTGTACATGATTCATGCTATTGACACAGAAGATAATAAGTATGATTTTGTGAATGAGATAGCAGCTGAGGCCAACGCTTATGTTGAGAGCAACATGGATGAGTATGGAGGTGAGAAGAAAGCCATTCTTCATGTTTTGAGTAATCGAGTGAATGATGCCGGATTTTACCGTCCAGAGGCGTATGCCGAGTCTGATCCCTTCAAACCTGGGCCTCATTATTTGAAAGAGTTTTATACATAA

Protein sequence

>MsG0380016544.01.T01

MVMLVYMIHAIDTEDNKYDFVNEIAAEANAYVESNMDEYGGEKKAILHVLSNRVNDAGFYRPEAYAESDPFKPGPHYLKEFYT*