AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0360540


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0360540 MtrunA17_Chr3g0098521 77.483 151 34 0 49 199 1 151 3.62e-84 246
Msa0360540 MtrunA17_Chr3g0098291 69.519 187 50 4 15 198 1 183 1.30e-83 247
Msa0360540 MtrunA17_Chr3g0098491 76.159 151 36 0 49 199 1 151 9.08e-82 239
Msa0360540 MtrunA17_Chr3g0102001 46.429 168 77 4 43 198 21 187 8.30e-36 132
Msa0360540 MtrunA17_Chr3g0098541 50.000 136 59 2 72 198 5 140 9.86e-34 123
Msa0360540 MtrunA17_Chr5g0439021 41.615 161 84 3 46 199 25 182 7.71e-33 116
Msa0360540 MtrunA17_Chr5g0439071 40.881 159 83 3 48 198 27 182 9.91e-28 109
Msa0360540 MtrunA17_Chr5g0439061 43.478 161 77 5 50 198 29 187 1.21e-25 103
Msa0360540 MtrunA17_Chr2g0286601 37.013 154 91 3 49 199 14 164 2.25e-17 79.7
Msa0360540 MtrunA17_Chr2g0286571 38.065 155 88 4 49 199 14 164 4.83e-17 77.8
Msa0360540 MtrunA17_Chr2g0286551 36.364 154 92 3 49 199 14 164 5.98e-16 75.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGGAGAAACACCACTCTTT+TGG 0.238209 3_1:-49964859 Msa0360540:CDS
TGAGACTGAATCATAGAATT+AGG 0.239693 3_1:+49965481 None:intergenic
TGAGGCTGAATCATAGAATT+AGG 0.314261 3_1:+49965523 None:intergenic
TAGAAATGAAAATAAGAATA+AGG 0.337200 3_1:+49965569 None:intergenic
TCATTGGAGAAGATGGTAAA+AGG 0.344288 3_1:-49964910 Msa0360540:CDS
TAAGTGTCAAACTTCTGAAA+TGG 0.365860 3_1:-49965548 Msa0360540:exon
TTCATCTTCATCTTCATCTT+CGG 0.366491 3_1:+49965450 None:intergenic
ATTTGTCTTCCATTACTAAC+TGG 0.368328 3_1:+49965170 None:intergenic
GCCATTCATAGAGAAATATT+CGG 0.388945 3_1:-49964731 Msa0360540:CDS
ATAGCAAGATTGATATCATA+TGG 0.409074 3_1:+49964785 None:intergenic
GTTAGTAATGGAAGACAAAT+GGG 0.435267 3_1:-49965167 Msa0360540:CDS
AGTTAGTAATGGAAGACAAA+TGG 0.436776 3_1:-49965168 Msa0360540:CDS
AGTATATGTGAATGTATCAT+TGG 0.446416 3_1:-49964926 Msa0360540:CDS
ACCGAATATTTCTCTATGAA+TGG 0.459441 3_1:+49964730 None:intergenic
AATAAGGATCAATGAGAGAT+GGG 0.472369 3_1:+49965585 None:intergenic
TTCATTTCATCTTCATCTTG+AGG 0.482522 3_1:+49965505 None:intergenic
CTTCATAGTGCAGCATATAG+AGG 0.496464 3_1:-49964956 Msa0360540:CDS
GATCAATGAGAGATGGGTAG+TGG 0.515618 3_1:+49965591 None:intergenic
GAATAAGGATCAATGAGAGA+TGG 0.522096 3_1:+49965584 None:intergenic
ATGAATGGCAACGTGAAGAA+TGG 0.528135 3_1:+49964745 None:intergenic
AAACTGATGTAGGTAAAGAA+AGG 0.539480 3_1:+49964811 None:intergenic
CGTGTTCCGCCAGTTAGTAA+TGG 0.552591 3_1:-49965179 Msa0360540:CDS
GTAAGCAATGCCTACAAAGA+TGG 0.555466 3_1:-49965061 Msa0360540:CDS
TAGCAAGATTGATATCATAT+GGG 0.563968 3_1:+49964786 None:intergenic
CTATATGCTGCACTATGAAG+AGG 0.567355 3_1:+49964959 None:intergenic
CATTACTAACTGGCGGAACA+CGG 0.570660 3_1:+49965180 None:intergenic
GAAGATTATGACTCTCAAGA+TGG 0.573204 3_1:-49965430 Msa0360540:intron
GACTTGTAGATGCAATAGAA+AGG 0.582410 3_1:-49965030 Msa0360540:CDS
GAATGTATCATTGGAGAAGA+TGG 0.599648 3_1:-49964917 Msa0360540:CDS
GAAAGGCATGGTGATCTAAG+TGG 0.601066 3_1:-49965013 Msa0360540:CDS
GCAAGCACAGCCCAAAAGAG+TGG 0.605571 3_1:+49964848 None:intergenic
AATCTTGCTATCAATAACAA+TGG 0.617874 3_1:-49964773 Msa0360540:CDS
TGTCTTCCATTACTAACTGG+CGG 0.631097 3_1:+49965173 None:intergenic
GTAGATGCAATAGAAAGGCA+TGG 0.659549 3_1:-49965025 Msa0360540:CDS
AAGAGGAACAGCATTACATG+TGG 0.700334 3_1:-49965086 Msa0360540:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAGAAATGAAAATAAGAATA+AGG + chr3_1:49964752-49964771 None:intergenic 15.0%
!! TTAATTAATCACAAAAATGT+TGG + chr3_1:49964969-49964988 None:intergenic 15.0%
!! TTAATGTCACATTAAAAAAT+TGG + chr3_1:49965070-49965089 None:intergenic 15.0%
!!! TTTTCACAAGATAAAAATAA+AGG - chr3_1:49965208-49965227 Msa0360540:intron 15.0%
!! TTTCACAAGATAAAAATAAA+GGG - chr3_1:49965209-49965228 Msa0360540:intron 15.0%
!! TAGAAATGAAAATAAGAATA+AGG + chr3_1:49964752-49964771 None:intergenic 15.0%
!! TTAATTAATCACAAAAATGT+TGG + chr3_1:49964969-49964988 None:intergenic 15.0%
!! TTAATGTCACATTAAAAAAT+TGG + chr3_1:49965070-49965089 None:intergenic 15.0%
!!! TTTTCACAAGATAAAAATAA+AGG - chr3_1:49965208-49965227 Msa0360540:intron 15.0%
!! TTTCACAAGATAAAAATAAA+GGG - chr3_1:49965209-49965228 Msa0360540:intron 15.0%
!! AATAAATATAAGGAGAGTTT+AGG + chr3_1:49964918-49964937 None:intergenic 20.0%
!! AAACTCTCCTTATATTTATT+AGG - chr3_1:49964918-49964937 Msa0360540:CDS 20.0%
!! ATTAGAGTAAAAAATGCAAA+GGG - chr3_1:49965440-49965459 Msa0360540:CDS 20.0%
!! AATAAATATAAGGAGAGTTT+AGG + chr3_1:49964918-49964937 None:intergenic 20.0%
!! AAACTCTCCTTATATTTATT+AGG - chr3_1:49964918-49964937 Msa0360540:CDS 20.0%
!! ATTAGAGTAAAAAATGCAAA+GGG - chr3_1:49965440-49965459 Msa0360540:CDS 20.0%
! TAAGGAGCCTAATAAATATA+AGG + chr3_1:49964928-49964947 None:intergenic 25.0%
! ATGTCACATTAAAAAATTGG+AGG + chr3_1:49965067-49965086 None:intergenic 25.0%
! AAGATAAAAATAAAGGGAAG+AGG - chr3_1:49965215-49965234 Msa0360540:intron 25.0%
! AGTATATGTGAATGTATCAT+TGG - chr3_1:49965392-49965411 Msa0360540:intron 25.0%
! GATTAGAGTAAAAAATGCAA+AGG - chr3_1:49965439-49965458 Msa0360540:CDS 25.0%
! TAGCAAGATTGATATCATAT+GGG + chr3_1:49965535-49965554 None:intergenic 25.0%
! ATAGCAAGATTGATATCATA+TGG + chr3_1:49965536-49965555 None:intergenic 25.0%
!! AATCTTGCTATCAATAACAA+TGG - chr3_1:49965545-49965564 Msa0360540:exon 25.0%
! TAAGGAGCCTAATAAATATA+AGG + chr3_1:49964928-49964947 None:intergenic 25.0%
! ATGTCACATTAAAAAATTGG+AGG + chr3_1:49965067-49965086 None:intergenic 25.0%
! AAGATAAAAATAAAGGGAAG+AGG - chr3_1:49965215-49965234 Msa0360540:intron 25.0%
! AGTATATGTGAATGTATCAT+TGG - chr3_1:49965392-49965411 Msa0360540:intron 25.0%
! GATTAGAGTAAAAAATGCAA+AGG - chr3_1:49965439-49965458 Msa0360540:CDS 25.0%
! TAGCAAGATTGATATCATAT+GGG + chr3_1:49965535-49965554 None:intergenic 25.0%
! ATAGCAAGATTGATATCATA+TGG + chr3_1:49965536-49965555 None:intergenic 25.0%
!! AATCTTGCTATCAATAACAA+TGG - chr3_1:49965545-49965564 Msa0360540:exon 25.0%
AATAAGGATCAATGAGAGAT+GGG + chr3_1:49964736-49964755 None:intergenic 30.0%
! TAAGTGTCAAACTTCTGAAA+TGG - chr3_1:49964770-49964789 Msa0360540:CDS 30.0%
TTCATTTCATCTTCATCTTG+AGG + chr3_1:49964816-49964835 None:intergenic 30.0%
TGAGACTGAATCATAGAATT+AGG + chr3_1:49964840-49964859 None:intergenic 30.0%
TTCATCTTCATCTTCATCTT+CGG + chr3_1:49964871-49964890 None:intergenic 30.0%
AAAGATTGAACGTCAACTTA+AGG + chr3_1:49964946-49964965 None:intergenic 30.0%
!! TTAGTCTTACTTCAATGATG+AGG - chr3_1:49965012-49965031 Msa0360540:CDS 30.0%
ATTTGTCTTCCATTACTAAC+TGG + chr3_1:49965151-49965170 None:intergenic 30.0%
! AGTTAGTAATGGAAGACAAA+TGG - chr3_1:49965150-49965169 Msa0360540:CDS 30.0%
! GTTAGTAATGGAAGACAAAT+GGG - chr3_1:49965151-49965170 Msa0360540:CDS 30.0%
! GGTAAAGAAAGGTCTTTTTA+TGG + chr3_1:49965499-49965518 None:intergenic 30.0%
AAACTGATGTAGGTAAAGAA+AGG + chr3_1:49965510-49965529 None:intergenic 30.0%
GCCATTCATAGAGAAATATT+CGG - chr3_1:49965587-49965606 Msa0360540:five_prime_UTR 30.0%
ACCGAATATTTCTCTATGAA+TGG + chr3_1:49965591-49965610 None:intergenic 30.0%
AATAAGGATCAATGAGAGAT+GGG + chr3_1:49964736-49964755 None:intergenic 30.0%
! TAAGTGTCAAACTTCTGAAA+TGG - chr3_1:49964770-49964789 Msa0360540:CDS 30.0%
TTCATTTCATCTTCATCTTG+AGG + chr3_1:49964816-49964835 None:intergenic 30.0%
TGAGACTGAATCATAGAATT+AGG + chr3_1:49964840-49964859 None:intergenic 30.0%
TTCATCTTCATCTTCATCTT+CGG + chr3_1:49964871-49964890 None:intergenic 30.0%
AAAGATTGAACGTCAACTTA+AGG + chr3_1:49964946-49964965 None:intergenic 30.0%
!! TTAGTCTTACTTCAATGATG+AGG - chr3_1:49965012-49965031 Msa0360540:CDS 30.0%
ATTTGTCTTCCATTACTAAC+TGG + chr3_1:49965151-49965170 None:intergenic 30.0%
! AGTTAGTAATGGAAGACAAA+TGG - chr3_1:49965150-49965169 Msa0360540:CDS 30.0%
! GTTAGTAATGGAAGACAAAT+GGG - chr3_1:49965151-49965170 Msa0360540:CDS 30.0%
! GGTAAAGAAAGGTCTTTTTA+TGG + chr3_1:49965499-49965518 None:intergenic 30.0%
AAACTGATGTAGGTAAAGAA+AGG + chr3_1:49965510-49965529 None:intergenic 30.0%
GCCATTCATAGAGAAATATT+CGG - chr3_1:49965587-49965606 Msa0360540:five_prime_UTR 30.0%
ACCGAATATTTCTCTATGAA+TGG + chr3_1:49965591-49965610 None:intergenic 30.0%
GAATAAGGATCAATGAGAGA+TGG + chr3_1:49964737-49964756 None:intergenic 35.0%
TGAGGCTGAATCATAGAATT+AGG + chr3_1:49964798-49964817 None:intergenic 35.0%
GAAGATTATGACTCTCAAGA+TGG - chr3_1:49964888-49964907 Msa0360540:CDS 35.0%
ACTTCAATGATGAGGCAATT+AGG - chr3_1:49965020-49965039 Msa0360540:CDS 35.0%
TGGAGGAAAAATTATGCACA+TGG + chr3_1:49965050-49965069 None:intergenic 35.0%
! TCGTTTTACACCATCTTTGT+AGG + chr3_1:49965270-49965289 None:intergenic 35.0%
GACTTGTAGATGCAATAGAA+AGG - chr3_1:49965288-49965307 Msa0360540:intron 35.0%
GAATGTATCATTGGAGAAGA+TGG - chr3_1:49965401-49965420 Msa0360540:intron 35.0%
TCATTGGAGAAGATGGTAAA+AGG - chr3_1:49965408-49965427 Msa0360540:intron 35.0%
CATATGGGAAAAACTGATGT+AGG + chr3_1:49965520-49965539 None:intergenic 35.0%
GAATAAGGATCAATGAGAGA+TGG + chr3_1:49964737-49964756 None:intergenic 35.0%
TGAGGCTGAATCATAGAATT+AGG + chr3_1:49964798-49964817 None:intergenic 35.0%
GAAGATTATGACTCTCAAGA+TGG - chr3_1:49964888-49964907 Msa0360540:CDS 35.0%
ACTTCAATGATGAGGCAATT+AGG - chr3_1:49965020-49965039 Msa0360540:CDS 35.0%
TGGAGGAAAAATTATGCACA+TGG + chr3_1:49965050-49965069 None:intergenic 35.0%
! TCGTTTTACACCATCTTTGT+AGG + chr3_1:49965270-49965289 None:intergenic 35.0%
GACTTGTAGATGCAATAGAA+AGG - chr3_1:49965288-49965307 Msa0360540:intron 35.0%
GAATGTATCATTGGAGAAGA+TGG - chr3_1:49965401-49965420 Msa0360540:intron 35.0%
TCATTGGAGAAGATGGTAAA+AGG - chr3_1:49965408-49965427 Msa0360540:intron 35.0%
CATATGGGAAAAACTGATGT+AGG + chr3_1:49965520-49965539 None:intergenic 35.0%
TGTCTTCCATTACTAACTGG+CGG + chr3_1:49965148-49965167 None:intergenic 40.0%
AAGAGGAACAGCATTACATG+TGG - chr3_1:49965232-49965251 Msa0360540:intron 40.0%
GTAAGCAATGCCTACAAAGA+TGG - chr3_1:49965257-49965276 Msa0360540:intron 40.0%
GTAGATGCAATAGAAAGGCA+TGG - chr3_1:49965293-49965312 Msa0360540:intron 40.0%
CTATATGCTGCACTATGAAG+AGG + chr3_1:49965362-49965381 None:intergenic 40.0%
CTTCATAGTGCAGCATATAG+AGG - chr3_1:49965362-49965381 Msa0360540:intron 40.0%
ATGAATGGCAACGTGAAGAA+TGG + chr3_1:49965576-49965595 None:intergenic 40.0%
TGTCTTCCATTACTAACTGG+CGG + chr3_1:49965148-49965167 None:intergenic 40.0%
AAGAGGAACAGCATTACATG+TGG - chr3_1:49965232-49965251 Msa0360540:intron 40.0%
GTAAGCAATGCCTACAAAGA+TGG - chr3_1:49965257-49965276 Msa0360540:intron 40.0%
GTAGATGCAATAGAAAGGCA+TGG - chr3_1:49965293-49965312 Msa0360540:intron 40.0%
CTATATGCTGCACTATGAAG+AGG + chr3_1:49965362-49965381 None:intergenic 40.0%
CTTCATAGTGCAGCATATAG+AGG - chr3_1:49965362-49965381 Msa0360540:intron 40.0%
ATGAATGGCAACGTGAAGAA+TGG + chr3_1:49965576-49965595 None:intergenic 40.0%
GATCAATGAGAGATGGGTAG+TGG + chr3_1:49964730-49964749 None:intergenic 45.0%
CATTACTAACTGGCGGAACA+CGG + chr3_1:49965141-49965160 None:intergenic 45.0%
! GAAAGGCATGGTGATCTAAG+TGG - chr3_1:49965305-49965324 Msa0360540:intron 45.0%
! AGGGAGAAACACCACTCTTT+TGG - chr3_1:49965459-49965478 Msa0360540:CDS 45.0%
! GGGAGAAACACCACTCTTTT+GGG - chr3_1:49965460-49965479 Msa0360540:CDS 45.0%
GATCAATGAGAGATGGGTAG+TGG + chr3_1:49964730-49964749 None:intergenic 45.0%
CATTACTAACTGGCGGAACA+CGG + chr3_1:49965141-49965160 None:intergenic 45.0%
! GAAAGGCATGGTGATCTAAG+TGG - chr3_1:49965305-49965324 Msa0360540:intron 45.0%
! AGGGAGAAACACCACTCTTT+TGG - chr3_1:49965459-49965478 Msa0360540:CDS 45.0%
! GGGAGAAACACCACTCTTTT+GGG - chr3_1:49965460-49965479 Msa0360540:CDS 45.0%
CGTGTTCCGCCAGTTAGTAA+TGG - chr3_1:49965139-49965158 Msa0360540:CDS 50.0%
CGTGTTCCGCCAGTTAGTAA+TGG - chr3_1:49965139-49965158 Msa0360540:CDS 50.0%
GCAAGCACAGCCCAAAAGAG+TGG + chr3_1:49965473-49965492 None:intergenic 55.0%
GCAAGCACAGCCCAAAAGAG+TGG + chr3_1:49965473-49965492 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 49964727 49965613 49964727 ID=Msa0360540;Name=Msa0360540
chr3_1 mRNA 49964727 49965613 49964727 ID=Msa0360540-mRNA-1;Parent=Msa0360540;Name=Msa0360540-mRNA-1;_AED=0.07;_eAED=0.07;_QI=62|1|0.5|1|1|1|2|0|199
chr3_1 exon 49964727 49965205 49964727 ID=Msa0360540-mRNA-1:exon:8801;Parent=Msa0360540-mRNA-1
chr3_1 exon 49965431 49965613 49965431 ID=Msa0360540-mRNA-1:exon:8800;Parent=Msa0360540-mRNA-1
chr3_1 five_prime_UTR 49965552 49965613 49965552 ID=Msa0360540-mRNA-1:five_prime_utr;Parent=Msa0360540-mRNA-1
chr3_1 CDS 49965431 49965551 49965431 ID=Msa0360540-mRNA-1:cds;Parent=Msa0360540-mRNA-1
chr3_1 CDS 49964727 49965205 49964727 ID=Msa0360540-mRNA-1:cds;Parent=Msa0360540-mRNA-1
Gene Sequence

>Msa0360540

ATGGATCCTAATTCTATGATTCAGCCTCAAGATGAAGATGAAATGAATCCTAATTCTATGATTCAGTCTCAAGATGATTCCGAAGATGAAGATGAAGATGAAGATTATGACTCTCAAGATGCTGCCGTGTTCCGCCAGTTAGTAATGGAAGACAAATGGGAAGAAGTAATCAAAAAATATGAAGAACATGTATTTTTTCACAAGATAAAAATAAAGGGAAGAGGAACAGCATTACATGTGGCAGTAAGCAATGCCTACAAAGATGGTGTAAAACGACTTGTAGATGCAATAGAAAGGCATGGTGATCTAAGTGGTTTAGAATTGTCAAATGAAAGAGATGCTACTCCTCTTCATAGTGCAGCATATAGAGGATTCACAAGTATATGTGAATGTATCATTGGAGAAGATGGTAAAAGGAAGCATTTGATTAGAGTAAAAAATGCAAAGGGAGAAACACCACTCTTTTGGGCTGTGCTTGCACGCCATAAAAAGACCTTTCTTTACCTACATCAGTTTTTCCCATATGATATCAATCTTGCTATCAATAACAATGGCACTACCATTCTTCACGTTGCCATTCATAGAGAAATATTCGGTTAG

Protein sequence

>Msa0360540

MDPNSMIQPQDEDEMNPNSMIQSQDDSEDEDEDEDYDSQDAAVFRQLVMEDKWEEVIKKYEEHVFFHKIKIKGRGTALHVAVSNAYKDGVKRLVDAIERHGDLSGLELSNERDATPLHSAAYRGFTSICECIIGEDGKRKHLIRVKNAKGETPLFWAVLARHKKTFLYLHQFFPYDINLAINNNGTTILHVAIHREIFG*