AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0349090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0349090 MtrunA17_Chr3g0085361 66.207 145 44 2 1 143 40 181 1.23e-59 188
Msa0349090 MtrunA17_Chr3g0085681 66.207 145 44 2 1 143 125 266 2.59e-58 187
Msa0349090 MtrunA17_Chr4g0038851 47.651 149 73 2 1 144 148 296 4.18e-36 129
Msa0349090 MtrunA17_Chr5g0396491 45.333 150 75 3 1 143 156 305 9.15e-33 120
Msa0349090 MtrunA17_Chr3g0087711 63.793 58 19 1 52 107 1 58 3.35e-15 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0349090 AT1G50420.1 42.763 152 79 3 1 145 159 309 5.12e-30 113

Find 25 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATGAAAAGAAAGATGTAT+TGG 0.432505 3_1:+12296990 Msa0349090:CDS
TTGTCAAACGAAAACTCATT+TGG 0.439065 3_1:-12297014 None:intergenic
AACTTTGGATTAATCTGTAA+AGG 0.444617 3_1:-12297060 None:intergenic
AGAAGATTTATACACTGGTC+TGG 0.460897 3_1:-12296913 None:intergenic
GCTGGGAGAATCTCACCAAC+AGG 0.486357 3_1:+12297194 Msa0349090:CDS
GCCGCTGATGATGAAACAGC+TGG 0.487530 3_1:+12297176 Msa0349090:CDS
TTTCGTTTGACAACGGAACC+AGG 0.490333 3_1:+12297024 Msa0349090:CDS
CTCTGCAGATTGATAAATGC+CGG 0.527470 3_1:-12297218 None:intergenic
TTTGTAGAAGATTTATACAC+TGG 0.531590 3_1:-12296918 None:intergenic
TGAATCAATGGAATGTGAAA+AGG 0.560459 3_1:+12296858 None:intergenic
CCCAGCTGTTTCATCATCAG+CGG 0.566236 3_1:-12297177 None:intergenic
GAGAATCTCACCAACAGGAC+CGG 0.575709 3_1:+12297199 Msa0349090:CDS
GTCAGAGGGATTTCGAAAAG+TGG 0.585911 3_1:+12297255 Msa0349090:CDS
TTGATAAATGCCGGTCCTGT+TGG 0.590041 3_1:-12297209 None:intergenic
AAAGGAAAATGCAAGTTCCC+TGG 0.591944 3_1:-12297042 None:intergenic
AACAGTACACATAAGTCAGA+GGG 0.595966 3_1:+12297241 Msa0349090:CDS
GAACAGTACACATAAGTCAG+AGG 0.608684 3_1:+12297240 Msa0349090:CDS
ACAAACTTCAAAGAAAAGTG+AGG 0.613226 3_1:+12296936 Msa0349090:CDS
TTCGTTTGACAACGGAACCA+GGG 0.615089 3_1:+12297025 Msa0349090:CDS
CAAACTTCAAAGAAAAGTGA+GGG 0.617757 3_1:+12296937 Msa0349090:CDS
CCGCTGATGATGAAACAGCT+GGG 0.622590 3_1:+12297177 Msa0349090:CDS
ATCAATGGAATGTGAAAAGG+TGG 0.652781 3_1:+12296861 None:intergenic
CTGTTTCATCATCAGCGGCG+AGG 0.673898 3_1:-12297172 None:intergenic
ACTTCAAAGAAAAGTGAGGG+AGG 0.680351 3_1:+12296940 Msa0349090:CDS
ACTGGTCTGGTTCAGAACAA+CGG 0.690931 3_1:-12296900 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCTTGTAATTTTCAGATA+GGG - chr3_1:12296970-12296989 None:intergenic 20.0%
!!! AATTCTTGTAATTTTCAGAT+AGG - chr3_1:12296971-12296990 None:intergenic 20.0%
! TTTGTAGAAGATTTATACAC+TGG - chr3_1:12296921-12296940 None:intergenic 25.0%
! TCATGAAAAGAAAGATGTAT+TGG + chr3_1:12296990-12297009 Msa0349090:CDS 25.0%
! AACTTTGGATTAATCTGTAA+AGG - chr3_1:12297063-12297082 None:intergenic 25.0%
!!! ATTTTTGAGTTTGCTAACTT+TGG - chr3_1:12297078-12297097 None:intergenic 25.0%
ACAAACTTCAAAGAAAAGTG+AGG + chr3_1:12296936-12296955 Msa0349090:CDS 30.0%
CAAACTTCAAAGAAAAGTGA+GGG + chr3_1:12296937-12296956 Msa0349090:CDS 30.0%
TTGTCAAACGAAAACTCATT+TGG - chr3_1:12297017-12297036 None:intergenic 30.0%
! AATGAGTTTTCGTTTGACAA+CGG + chr3_1:12297017-12297036 Msa0349090:CDS 30.0%
AGAAGATTTATACACTGGTC+TGG - chr3_1:12296916-12296935 None:intergenic 35.0%
! CTTGTAATTTTCAGATAGGG+TGG - chr3_1:12296967-12296986 None:intergenic 35.0%
AACAGTACACATAAGTCAGA+GGG + chr3_1:12297241-12297260 Msa0349090:CDS 35.0%
ACTTCAAAGAAAAGTGAGGG+AGG + chr3_1:12296940-12296959 Msa0349090:CDS 40.0%
AAAGGAAAATGCAAGTTCCC+TGG - chr3_1:12297045-12297064 None:intergenic 40.0%
CTCTGCAGATTGATAAATGC+CGG - chr3_1:12297221-12297240 None:intergenic 40.0%
GAACAGTACACATAAGTCAG+AGG + chr3_1:12297240-12297259 Msa0349090:CDS 40.0%
! ACTGGTCTGGTTCAGAACAA+CGG - chr3_1:12296903-12296922 None:intergenic 45.0%
TTTCGTTTGACAACGGAACC+AGG + chr3_1:12297024-12297043 Msa0349090:CDS 45.0%
TTCGTTTGACAACGGAACCA+GGG + chr3_1:12297025-12297044 Msa0349090:CDS 45.0%
TTGATAAATGCCGGTCCTGT+TGG - chr3_1:12297212-12297231 None:intergenic 45.0%
GTCAGAGGGATTTCGAAAAG+TGG + chr3_1:12297255-12297274 Msa0349090:CDS 45.0%
! CCCAGCTGTTTCATCATCAG+CGG - chr3_1:12297180-12297199 None:intergenic 50.0%
! CCGCTGATGATGAAACAGCT+GGG + chr3_1:12297177-12297196 Msa0349090:CDS 50.0%
GAGAATCTCACCAACAGGAC+CGG + chr3_1:12297199-12297218 Msa0349090:CDS 50.0%
CTGTTTCATCATCAGCGGCG+AGG - chr3_1:12297175-12297194 None:intergenic 55.0%
! GCCGCTGATGATGAAACAGC+TGG + chr3_1:12297176-12297195 Msa0349090:CDS 55.0%
GCTGGGAGAATCTCACCAAC+AGG + chr3_1:12297194-12297213 Msa0349090:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 12296865 12297328 12296865 ID=Msa0349090;Name=Msa0349090
chr3_1 mRNA 12296865 12297328 12296865 ID=Msa0349090-mRNA-1;Parent=Msa0349090;Name=Msa0349090-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|0|0|1|1|1|2|0|152
chr3_1 exon 12296865 12297079 12296865 ID=Msa0349090-mRNA-1:exon:3214;Parent=Msa0349090-mRNA-1
chr3_1 exon 12297085 12297328 12297085 ID=Msa0349090-mRNA-1:exon:3215;Parent=Msa0349090-mRNA-1
chr3_1 CDS 12296865 12297079 12296865 ID=Msa0349090-mRNA-1:cds;Parent=Msa0349090-mRNA-1
chr3_1 CDS 12297085 12297328 12297085 ID=Msa0349090-mRNA-1:cds;Parent=Msa0349090-mRNA-1
Gene Sequence

>Msa0349090

ATGGAATGTGAAAAGGTGGTTCAAATTATTGATCTCCGTTGTTCTGAACCAGACCAGTGTATAAATCTTCTACAAACTTCAAAGAAAAGTGAGGGAGGTCCACCCTATCTGAAAATTACAAGAATTCATGAAAAGAAAGATGTATTGGACCAAATGAGTTTTCGTTTGACAACGGAACCAGGGAACTTGCATTTTCCTTTACAGATTAATCCAAACAAACTCAAAAATGTCAATTTCGAAAACTTGTCTGTGAAGACAGAAGATGCTGTCGTTATTACTTCTGTTCTTCAGCTGCATTCTCTCCTCGCCGCTGATGATGAAACAGCTGGGAGAATCTCACCAACAGGACCGGCATTTATCAATCTGCAGAGAACAGTACACATAAGTCAGAGGGATTTCGAAAAGTGGCTCGAGAGAGATATGATCAATGATAATCAACAAGATTTCAAGATTTCTTAA
Protein sequence

>Msa0349090

MECEKVVQIIDLRCSEPDQCINLLQTSKKSEGGPPYLKITRIHEKKDVLDQMSFRLTTEPGNLHFPLQINPNKLKNVNFENLSVKTEDAVVITSVLQLHSLLAADDETAGRISPTGPAFINLQRTVHISQRDFEKWLERDMINDNQQDFKIS*