AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394170


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394170 MtrunA17_CPg0492991 97.309 223 6 0 1 223 14 236 1.51e-164 453
Msa1394170 MtrunA17_Chr4g0015601 97.309 223 6 0 1 223 14 236 1.60e-164 453
Msa1394170 MtrunA17_Chr4g0016691 98.496 133 2 0 91 223 1 133 3.35e-95 274
Msa1394170 MtrunA17_Chr7g0275161 90.722 97 9 0 127 223 1 97 3.30e-60 184
Msa1394170 MtrunA17_Chr7g0275171 80.233 86 7 1 1 86 14 89 6.88e-44 142
Msa1394170 MtrunA17_Chr4g0016681 96.970 66 2 0 1 66 14 79 2.56e-42 138
Msa1394170 MtrunA17_Chr1g0178511 97.143 35 1 0 91 125 1 35 1.49e-16 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394170 ATCG00160.1 89.640 222 23 0 1 222 14 235 2.05e-148 412

Find 37 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTCATTTGGAAACATATC+TGG 0.181531 tig0021785:-74152 Msa1394170:CDS
TTACGCTTTGCCGATATAAA+AGG 0.251568 tig0021785:+74490 None:intergenic
ATGGAAGCTGGAGTTCATTT+TGG 0.255790 tig0021785:-74547 Msa1394170:CDS
CAAGAGACAATTATCTCATT+TGG 0.294663 tig0021785:-74164 Msa1394170:CDS
ATCAACGATTATTACAATAT+CGG 0.341941 tig0021785:+74102 None:intergenic
TTTATCAGAAGCTTGTGATT+TGG 0.358806 tig0021785:-74428 Msa1394170:CDS
CTAATTTGTTAAGAATTAAT+CGG 0.359442 tig0021785:+73945 None:intergenic
ATCGAAATATCTGCTAGATC+TGG 0.363586 tig0021785:+73998 None:intergenic
CTTCGAGAATGTATCACTTT+GGG 0.388824 tig0021785:-74058 Msa1394170:CDS
GGAAAACAATTCTTAATTGT+TGG 0.390734 tig0021785:-74385 Msa1394170:CDS
AAACGAGACTTCGTAAGTTC+AGG 0.412190 tig0021785:-74252 Msa1394170:CDS
TGCAGCCCGTGTTACTGAAT+CGG 0.431042 tig0021785:+74345 None:intergenic
TGATCAGCAAGAAGAATATA+CGG 0.437056 tig0021785:-74083 Msa1394170:CDS
TCGGAGGTATGTTAACGAAT+TGG 0.448395 tig0021785:-74285 Msa1394170:CDS
TTGGCCATGATACTCGGAAA+TGG 0.459897 tig0021785:-74528 Msa1394170:CDS
TCTTCGAGAATGTATCACTT+TGG 0.477646 tig0021785:-74059 Msa1394170:CDS
AACGAGACTTCGTAAGTTCA+GGG 0.478021 tig0021785:-74251 Msa1394170:CDS
TCAACGATTATTACAATATC+GGG 0.480431 tig0021785:+74103 None:intergenic
TTGAGAACGGAGCAAAAGAC+AGG 0.482432 tig0021785:-74226 Msa1394170:CDS
GATTCCATTTCCGAGTATCA+TGG 0.488914 tig0021785:+74524 None:intergenic
TTTGAAGAGATGATGGAAGC+TGG 0.489132 tig0021785:-74559 None:intergenic
GTATCGATTAAACAAATCGT+TGG 0.491426 tig0021785:+74031 None:intergenic
GCTATAGCATCATCATTAGC+TGG 0.518853 tig0021785:+73974 None:intergenic
TCGAAATATCTGCTAGATCT+GGG 0.525094 tig0021785:+73999 None:intergenic
TTTATATCGGCAAAGCGTAA+AGG 0.529937 tig0021785:-74487 Msa1394170:CDS
GATATAAAAGGTGCCATTCG+AGG 0.542260 tig0021785:+74502 None:intergenic
TCTCATTTGGAAACATATCT+GGG 0.550552 tig0021785:-74151 Msa1394170:CDS
GGGTGGCATAAAATATATGA+CGG 0.585418 tig0021785:-74131 Msa1394170:CDS
TAAGTTCAGGGACTTGAGAA+CGG 0.589134 tig0021785:-74239 Msa1394170:CDS
GGTGGCATAAAATATATGAC+GGG 0.610359 tig0021785:-74130 Msa1394170:CDS
AGCAGCCGATTCAGTAACAC+GGG 0.610911 tig0021785:-74350 Msa1394170:CDS
TCGGAAATGGAATCCTCGAA+TGG 0.635386 tig0021785:-74515 Msa1394170:CDS
AAGCAGCCGATTCAGTAACA+CGG 0.653513 tig0021785:-74351 Msa1394170:CDS
TGAGAACGGAGCAAAAGACA+GGG 0.670658 tig0021785:-74225 Msa1394170:CDS
CATTTGGAAACATATCTGGG+TGG 0.732935 tig0021785:-74148 Msa1394170:CDS
GTGGCATAAAATATATGACG+GGG 0.737363 tig0021785:-74129 Msa1394170:CDS
TAATTGTCTCTTGAACATAG+CGG 0.783646 tig0021785:+74174 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTCATTATGTTAATAAAAAA+TGG - tig0021785:74136-74155 Msa1394170:CDS 15.0%
!!! CTAATTTGTTAAGAATTAAT+CGG + tig0021785:74503-74522 None:intergenic 15.0%
!! TATGTTAATAAAAAATGGCT+CGG - tig0021785:74141-74160 Msa1394170:CDS 20.0%
!! ATCAACGATTATTACAATAT+CGG + tig0021785:74346-74365 None:intergenic 20.0%
! GGAAAACAATTCTTAATTGT+TGG - tig0021785:74060-74079 Msa1394170:CDS 25.0%
! TCAACGATTATTACAATATC+GGG + tig0021785:74345-74364 None:intergenic 25.0%
!!! ATTAGTTTTTGCAATTTGTG+AGG - tig0021785:74518-74537 Msa1394170:CDS 25.0%
!!! TTAGTTTTTGCAATTTGTGA+GGG - tig0021785:74519-74538 Msa1394170:CDS 25.0%
TTTATCAGAAGCTTGTGATT+TGG - tig0021785:74017-74036 Msa1394170:CDS 30.0%
TAATTGTCTCTTGAACATAG+CGG + tig0021785:74274-74293 None:intergenic 30.0%
CAAGAGACAATTATCTCATT+TGG - tig0021785:74281-74300 Msa1394170:CDS 30.0%
ATCTCATTTGGAAACATATC+TGG - tig0021785:74293-74312 Msa1394170:CDS 30.0%
TCTCATTTGGAAACATATCT+GGG - tig0021785:74294-74313 Msa1394170:CDS 30.0%
TGATCAGCAAGAAGAATATA+CGG - tig0021785:74362-74381 Msa1394170:CDS 30.0%
!! GTATCGATTAAACAAATCGT+TGG + tig0021785:74417-74436 None:intergenic 30.0%
!! TTCATTTTGGCCATGATACT+CGG - tig0021785:73911-73930 Msa1394170:CDS 35.0%
! TCGAATGGCACCTTTTATAT+CGG - tig0021785:73945-73964 Msa1394170:CDS 35.0%
TTACGCTTTGCCGATATAAA+AGG + tig0021785:73958-73977 None:intergenic 35.0%
TTTATATCGGCAAAGCGTAA+AGG - tig0021785:73958-73977 Msa1394170:CDS 35.0%
! GTTAATAAAAAATGGCTCGG+AGG - tig0021785:74144-74163 Msa1394170:CDS 35.0%
GGGTGGCATAAAATATATGA+CGG - tig0021785:74314-74333 Msa1394170:CDS 35.0%
GGTGGCATAAAATATATGAC+GGG - tig0021785:74315-74334 Msa1394170:CDS 35.0%
GTGGCATAAAATATATGACG+GGG - tig0021785:74316-74335 Msa1394170:CDS 35.0%
TCTTCGAGAATGTATCACTT+TGG - tig0021785:74386-74405 Msa1394170:CDS 35.0%
CTTCGAGAATGTATCACTTT+GGG - tig0021785:74387-74406 Msa1394170:CDS 35.0%
TCGAAATATCTGCTAGATCT+GGG + tig0021785:74449-74468 None:intergenic 35.0%
ATCGAAATATCTGCTAGATC+TGG + tig0021785:74450-74469 None:intergenic 35.0%
! ATGGAAGCTGGAGTTCATTT+TGG - tig0021785:73898-73917 Msa1394170:CDS 40.0%
GATTCCATTTCCGAGTATCA+TGG + tig0021785:73924-73943 None:intergenic 40.0%
!! GATATAAAAGGTGCCATTCG+AGG + tig0021785:73946-73965 None:intergenic 40.0%
! GTTTTTGATGCAGCAAGCAT+GGG - tig0021785:74039-74058 Msa1394170:CDS 40.0%
! TCGGAGGTATGTTAACGAAT+TGG - tig0021785:74160-74179 Msa1394170:CDS 40.0%
AAACGAGACTTCGTAAGTTC+AGG - tig0021785:74193-74212 Msa1394170:CDS 40.0%
AACGAGACTTCGTAAGTTCA+GGG - tig0021785:74194-74213 Msa1394170:CDS 40.0%
TAAGTTCAGGGACTTGAGAA+CGG - tig0021785:74206-74225 Msa1394170:CDS 40.0%
! AACATAGCGGCATCTCTTTT+TGG + tig0021785:74261-74280 None:intergenic 40.0%
CATTTGGAAACATATCTGGG+TGG - tig0021785:74297-74316 Msa1394170:CDS 40.0%
GCTATAGCATCATCATTAGC+TGG + tig0021785:74474-74493 None:intergenic 40.0%
TTGGCCATGATACTCGGAAA+TGG - tig0021785:73917-73936 Msa1394170:CDS 45.0%
TCGGAAATGGAATCCTCGAA+TGG - tig0021785:73930-73949 Msa1394170:CDS 45.0%
! GGTTTTTGATGCAGCAAGCA+TGG - tig0021785:74038-74057 Msa1394170:CDS 45.0%
! AAGCAGCCGATTCAGTAACA+CGG - tig0021785:74094-74113 Msa1394170:CDS 45.0%
TTGAGAACGGAGCAAAAGAC+AGG - tig0021785:74219-74238 Msa1394170:CDS 45.0%
TGAGAACGGAGCAAAAGACA+GGG - tig0021785:74220-74239 Msa1394170:CDS 45.0%
! AGCAGCCGATTCAGTAACAC+GGG - tig0021785:74095-74114 Msa1394170:CDS 50.0%
! TGCAGCCCGTGTTACTGAAT+CGG + tig0021785:74103-74122 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0021785 gene 73898 74569 73898 ID=Msa1394170;Name=Msa1394170
tig0021785 mRNA 73898 74569 73898 ID=Msa1394170-mRNA-1;Parent=Msa1394170;Name=Msa1394170-mRNA-1;_AED=0.45;_eAED=0.45;_QI=0|-1|0|1|-1|1|1|0|223
tig0021785 exon 73898 74569 73898 ID=Msa1394170-mRNA-1:exon:14203;Parent=Msa1394170-mRNA-1
tig0021785 CDS 73898 74569 73898 ID=Msa1394170-mRNA-1:cds;Parent=Msa1394170-mRNA-1
Gene Sequence

>Msa1394170

ATGGAAGCTGGAGTTCATTTTGGCCATGATACTCGGAAATGGAATCCTCGAATGGCACCTTTTATATCGGCAAAGCGTAAAGGTATTCATATTACAAATCTTACTCGAACTGCTCGTTTTTTATCAGAAGCTTGTGATTTGGTTTTTGATGCAGCAAGCATGGGAAAACAATTCTTAATTGTTGGTACAAAAAAAAAAGCAGCCGATTCAGTAACACGGGCTGCAATAAGAGCTCGATGTCATTATGTTAATAAAAAATGGCTCGGAGGTATGTTAACGAATTGGTATACTACAGAAACGAGACTTCGTAAGTTCAGGGACTTGAGAACGGAGCAAAAGACAGGGAAACTGAACTCTCTTCCAAAAAGAGATGCCGCTATGTTCAAGAGACAATTATCTCATTTGGAAACATATCTGGGTGGCATAAAATATATGACGGGGTTACCCGATATTGTAATAATCGTTGATCAGCAAGAAGAATATACGGCTCTTCGAGAATGTATCACTTTGGGAATTCCAACGATTTGTTTAATCGATACAAATTGTGACCCAGATCTAGCAGATATTTCGATTCCAGCTAATGATGATGCTATAGCTTCAATCCGATTAATTCTTAACAAATTAGTTTTTGCAATTTGTGAGGGTCGTTCTAGCTATATACGAAATTTTTGA

Protein sequence

>Msa1394170

MEAGVHFGHDTRKWNPRMAPFISAKRKGIHITNLTRTARFLSEACDLVFDAASMGKQFLIVGTKKKAADSVTRAAIRARCHYVNKKWLGGMLTNWYTTETRLRKFRDLRTEQKTGKLNSLPKRDAAMFKRQLSHLETYLGGIKYMTGLPDIVIIVDQQEEYTALRECITLGIPTICLIDTNCDPDLADISIPANDDAIASIRLILNKLVFAICEGRSSYIRNF*