AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0448080


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0448080 MtrunA17_Chr3g0090001 95.455 154 7 0 1 154 250 403 2.96e-93 275
Msa0448080 MtrunA17_Chr3g0089951 96.000 100 4 0 1 100 1 100 7.06e-57 173
Msa0448080 MtrunA17_Chr7g0264491 33.333 153 102 0 1 153 401 553 3.71e-19 83.2
Msa0448080 MtrunA17_Chr3g0145921 29.801 151 106 0 4 154 421 571 1.86e-16 75.5
Msa0448080 MtrunA17_Chr1g0146481 31.373 153 98 2 2 153 401 547 6.24e-15 70.9
Msa0448080 MtrunA17_Chr4g0021031 37.313 134 67 4 20 142 363 490 1.80e-14 69.7
Msa0448080 MtrunA17_Chr1g0180881 29.605 152 107 0 2 153 406 557 3.45e-14 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0448080 AT5G13730.1 57.237 152 65 0 1 152 263 414 4.03e-53 173
Msa0448080 AT2G36990.1 30.065 153 107 0 1 153 391 543 7.28e-18 79.7
Msa0448080 AT1G08540.1 28.477 151 108 0 4 154 419 569 1.77e-15 72.8
Msa0448080 AT3G53920.1 32.308 130 88 0 24 153 440 569 3.01e-15 72.4
Msa0448080 AT1G64860.1 37.209 129 74 3 20 142 361 488 5.27e-13 65.9

Find 30 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAGCTCTGTCCAATGAAAT+TGG 0.288432 3_3:+27214224 None:intergenic
CGGAATCATTTCAACTGGTC+CGG 0.390258 3_3:+27214048 None:intergenic
ATATTATACTTTGGACTCAA+TGG 0.405310 3_3:-27213941 Msa0448080:CDS
TTCTCCGGAATCATTTCAAC+TGG 0.416683 3_3:+27214043 None:intergenic
GAGCAGACAACCAATTTCAT+TGG 0.418328 3_3:-27214234 Msa0448080:CDS
CGGACCAGTTGAAATGATTC+CGG 0.418554 3_3:-27214047 Msa0448080:CDS
GAGAGGCAGTTAGTGAAGGA+AGG 0.433775 3_3:-27214013 Msa0448080:CDS
GAGATTGTAATATTATACTT+TGG 0.445378 3_3:-27213950 Msa0448080:CDS
AGAGGCAGTTAGTGAAGGAA+GGG 0.449418 3_3:-27214012 Msa0448080:CDS
CTATCTCCTCAAAAGACAAA+GGG 0.452640 3_3:+27213912 None:intergenic
GAAAGCTGTTGAAACTATCA+AGG 0.471546 3_3:-27213889 Msa0448080:CDS
TGAAATGATTCCGGAGAAGA+TGG 0.476752 3_3:-27214038 Msa0448080:CDS
GAGAGGATCAGACAGATTCA+TGG 0.512718 3_3:-27213866 Msa0448080:CDS
TGCCTCTCAACCATCTTCTC+CGG 0.517628 3_3:+27214028 None:intergenic
CAGTATTAAGTTGCTCTGAT+CGG 0.520178 3_3:+27214199 None:intergenic
GGTTGAGAGGCAGTTAGTGA+AGG 0.524287 3_3:-27214017 Msa0448080:CDS
GAGGCAGTTAGTGAAGGAAG+GGG 0.526111 3_3:-27214011 Msa0448080:CDS
GGAATCATTTCAACTGGTCC+GGG 0.532057 3_3:+27214049 None:intergenic
CTGTAAAACTTGTTTCTGAA+AGG 0.534187 3_3:-27214256 Msa0448080:CDS
CCTATCTCCTCAAAAGACAA+AGG 0.538706 3_3:+27213911 None:intergenic
TCAGCAATTTCATTATATGT+CGG 0.554776 3_3:+27214302 None:intergenic
ATGTCTTAAGACGAAGACTA+AGG 0.570194 3_3:-27214331 Msa0448080:CDS
TGTTGAAACTATCAAGGGAG+AGG 0.571469 3_3:-27213883 Msa0448080:CDS
TCAGAGCAACTTAATACTGA+AGG 0.606839 3_3:-27214195 Msa0448080:intron
TTCCGGAGAAGATGGTTGAG+AGG 0.622689 3_3:-27214030 Msa0448080:CDS
AAAGCTGTTGAAACTATCAA+GGG 0.636294 3_3:-27213888 Msa0448080:CDS
ATAATGCAGGAGATTATACC+CGG 0.639702 3_3:-27214067 Msa0448080:intron
GACATATAATGAAATTGCTG+AGG 0.644481 3_3:-27214300 Msa0448080:CDS
TATCTCCTCAAAAGACAAAG+GGG 0.686203 3_3:+27213913 None:intergenic
TCTTAAGACGAAGACTAAGG+CGG 0.687494 3_3:-27214328 Msa0448080:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAATTTCATTTGTACTTT+AGG - chr3_3:27213992-27214011 Msa0448080:CDS 20.0%
!! GAGATTGTAATATTATACTT+TGG - chr3_3:27214211-27214230 Msa0448080:CDS 20.0%
! TCAGCAATTTCATTATATGT+CGG + chr3_3:27213862-27213881 None:intergenic 25.0%
! TCTTTACTATGATATAATGC+AGG - chr3_3:27214081-27214100 Msa0448080:intron 25.0%
! ATATTATACTTTGGACTCAA+TGG - chr3_3:27214220-27214239 Msa0448080:CDS 25.0%
GACATATAATGAAATTGCTG+AGG - chr3_3:27213861-27213880 Msa0448080:CDS 30.0%
!! CTGTAAAACTTGTTTCTGAA+AGG - chr3_3:27213905-27213924 Msa0448080:CDS 30.0%
AAAGCTGTTGAAACTATCAA+GGG - chr3_3:27214273-27214292 Msa0448080:CDS 30.0%
ATGTCTTAAGACGAAGACTA+AGG - chr3_3:27213830-27213849 Msa0448080:CDS 35.0%
! ATAGCTCTGTCCAATGAAAT+TGG + chr3_3:27213940-27213959 None:intergenic 35.0%
! CAGTATTAAGTTGCTCTGAT+CGG + chr3_3:27213965-27213984 None:intergenic 35.0%
TCAGAGCAACTTAATACTGA+AGG - chr3_3:27213966-27213985 Msa0448080:CDS 35.0%
ATAATGCAGGAGATTATACC+CGG - chr3_3:27214094-27214113 Msa0448080:intron 35.0%
TATCTCCTCAAAAGACAAAG+GGG + chr3_3:27214251-27214270 None:intergenic 35.0%
CTATCTCCTCAAAAGACAAA+GGG + chr3_3:27214252-27214271 None:intergenic 35.0%
GAAAGCTGTTGAAACTATCA+AGG - chr3_3:27214272-27214291 Msa0448080:CDS 35.0%
TCTTAAGACGAAGACTAAGG+CGG - chr3_3:27213833-27213852 Msa0448080:CDS 40.0%
GAGCAGACAACCAATTTCAT+TGG - chr3_3:27213927-27213946 Msa0448080:CDS 40.0%
TTCTCCGGAATCATTTCAAC+TGG + chr3_3:27214121-27214140 None:intergenic 40.0%
TGAAATGATTCCGGAGAAGA+TGG - chr3_3:27214123-27214142 Msa0448080:intron 40.0%
CCTATCTCCTCAAAAGACAA+AGG + chr3_3:27214253-27214272 None:intergenic 40.0%
!! CCTTTGTCTTTTGAGGAGAT+AGG - chr3_3:27214250-27214269 Msa0448080:CDS 40.0%
TGTTGAAACTATCAAGGGAG+AGG - chr3_3:27214278-27214297 Msa0448080:CDS 40.0%
GGAATCATTTCAACTGGTCC+GGG + chr3_3:27214115-27214134 None:intergenic 45.0%
CGGAATCATTTCAACTGGTC+CGG + chr3_3:27214116-27214135 None:intergenic 45.0%
CGGACCAGTTGAAATGATTC+CGG - chr3_3:27214114-27214133 Msa0448080:intron 45.0%
AGAGGCAGTTAGTGAAGGAA+GGG - chr3_3:27214149-27214168 Msa0448080:intron 45.0%
! AGAGACCCCTTTGTCTTTTG+AGG - chr3_3:27214243-27214262 Msa0448080:CDS 45.0%
GAGAGGATCAGACAGATTCA+TGG - chr3_3:27214295-27214314 Msa0448080:CDS 45.0%
TTCCGGAGAAGATGGTTGAG+AGG - chr3_3:27214131-27214150 Msa0448080:intron 50.0%
TGCCTCTCAACCATCTTCTC+CGG + chr3_3:27214136-27214155 None:intergenic 50.0%
GGTTGAGAGGCAGTTAGTGA+AGG - chr3_3:27214144-27214163 Msa0448080:intron 50.0%
GAGAGGCAGTTAGTGAAGGA+AGG - chr3_3:27214148-27214167 Msa0448080:intron 50.0%
GAGGCAGTTAGTGAAGGAAG+GGG - chr3_3:27214150-27214169 Msa0448080:intron 50.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 27213802 27214381 27213802 ID=Msa0448080;Name=Msa0448080
chr3_3 mRNA 27213802 27214381 27213802 ID=Msa0448080-mRNA-1;Parent=Msa0448080;Name=Msa0448080-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|154
chr3_3 exon 27214196 27214381 27214196 ID=Msa0448080-mRNA-1:exon:5329;Parent=Msa0448080-mRNA-1
chr3_3 exon 27213802 27214080 27213802 ID=Msa0448080-mRNA-1:exon:5328;Parent=Msa0448080-mRNA-1
chr3_3 CDS 27214196 27214381 27214196 ID=Msa0448080-mRNA-1:cds;Parent=Msa0448080-mRNA-1
chr3_3 CDS 27213802 27214080 27213802 ID=Msa0448080-mRNA-1:cds;Parent=Msa0448080-mRNA-1
Gene Sequence

>Msa0448080

ATGGTTGCAAAAATCGCAGAGGCTAACAATGTCTTAAGACGAAGACTAAGGCGGAAGCCGACATATAATGAAATTGCTGAGGTTCTCAATGTGAATGTTTCAACTGTAAAACTTGTTTCTGAAAGGAGCAGACAACCAATTTCATTGGACAGAGCTATAACCGATCAGAGCAACTTAATACTGAAGGAGATTATACCCGGACCAGTTGAAATGATTCCGGAGAAGATGGTTGAGAGGCAGTTAGTGAAGGAAGGGGTTGTGAAGCTTCTTAACACACTTAACAAGAGAGAAGAAGAGATTGTAATATTATACTTTGGACTCAATGGAGAGACCCCTTTGTCTTTTGAGGAGATAGGAAAGCTGTTGAAACTATCAAGGGAGAGGATCAGACAGATTCATGGTATTGCATTGTCAAAATTGCAACAAAATTTACTTGTAGATAGTCTAAAGTTTTATGTTGTATAG

Protein sequence

>Msa0448080

MVAKIAEANNVLRRRLRRKPTYNEIAEVLNVNVSTVKLVSERSRQPISLDRAITDQSNLILKEIIPGPVEMIPEKMVERQLVKEGVVKLLNTLNKREEEIVILYFGLNGETPLSFEEIGKLLKLSRERIRQIHGIALSKLQQNLLVDSLKFYVV*