AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086260 MtrunA17_CPg0492991 97.309 223 6 0 1 223 14 236 1.51e-164 453
Msa1086260 MtrunA17_Chr4g0015601 97.309 223 6 0 1 223 14 236 1.60e-164 453
Msa1086260 MtrunA17_Chr4g0016691 98.496 133 2 0 91 223 1 133 3.35e-95 274
Msa1086260 MtrunA17_Chr7g0275161 90.722 97 9 0 127 223 1 97 3.30e-60 184
Msa1086260 MtrunA17_Chr7g0275171 80.233 86 7 1 1 86 14 89 6.88e-44 142
Msa1086260 MtrunA17_Chr4g0016681 96.970 66 2 0 1 66 14 79 2.56e-42 138
Msa1086260 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
Msa1086260 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 7_2:+87295301 Msa1086260:CDS
TTACGCTTTGCCGATATAAA+AGG 0.251568 7_2:-87294963 None:intergenic
ATGGAAGCTGGAGTTCATTT+TGG 0.255790 7_2:+87294906 Msa1086260:CDS
CAAGAGACAATTATCTCATT+TGG 0.294663 7_2:+87295289 Msa1086260:CDS
ATCAACGATTATTACAATAT+CGG 0.341941 7_2:-87295351 None:intergenic
TTTATCAGAAGCTTGTGATT+TGG 0.358806 7_2:+87295025 Msa1086260:CDS
CTAATTTGTTAAGAATTAAT+CGG 0.359442 7_2:-87295508 None:intergenic
ATCGAAATATCTGCTAGATC+TGG 0.363586 7_2:-87295455 None:intergenic
CTTCGAGAATGTATCACTTT+GGG 0.388824 7_2:+87295395 Msa1086260:CDS
GGAAAACAATTCTTAATTGT+TGG 0.390734 7_2:+87295068 Msa1086260:CDS
AAACGAGACTTCGTAAGTTC+AGG 0.412190 7_2:+87295201 Msa1086260:CDS
TGCAGCCCGTGTTACTGAAT+CGG 0.431042 7_2:-87295108 None:intergenic
TGATCAGCAAGAAGAATATA+CGG 0.437056 7_2:+87295370 Msa1086260:CDS
TCGGAGGTATGTTAACGAAT+TGG 0.448395 7_2:+87295168 Msa1086260:CDS
TTGGCCATGATACTCGGAAA+TGG 0.459897 7_2:+87294925 Msa1086260:CDS
TCTTCGAGAATGTATCACTT+TGG 0.477646 7_2:+87295394 Msa1086260:CDS
AACGAGACTTCGTAAGTTCA+GGG 0.478021 7_2:+87295202 Msa1086260:CDS
TCAACGATTATTACAATATC+GGG 0.480431 7_2:-87295350 None:intergenic
TTGAGAACGGAGCAAAAGAC+AGG 0.482432 7_2:+87295227 Msa1086260:CDS
GATTCCATTTCCGAGTATCA+TGG 0.488914 7_2:-87294929 None:intergenic
TTTGAAGAGATGATGGAAGC+TGG 0.489132 7_2:+87294894 None:intergenic
GTATCGATTAAACAAATCGT+TGG 0.491426 7_2:-87295422 None:intergenic
GCTATAGCATCATCATTAGC+TGG 0.518853 7_2:-87295479 None:intergenic
TCGAAATATCTGCTAGATCT+GGG 0.525094 7_2:-87295454 None:intergenic
TTTATATCGGCAAAGCGTAA+AGG 0.529937 7_2:+87294966 Msa1086260:CDS
GATATAAAAGGTGCCATTCG+AGG 0.542260 7_2:-87294951 None:intergenic
TCTCATTTGGAAACATATCT+GGG 0.550552 7_2:+87295302 Msa1086260:CDS
GGGTGGCATAAAATATATGA+CGG 0.585418 7_2:+87295322 Msa1086260:CDS
TAAGTTCAGGGACTTGAGAA+CGG 0.589134 7_2:+87295214 Msa1086260:CDS
GGTGGCATAAAATATATGAC+GGG 0.610359 7_2:+87295323 Msa1086260:CDS
AGCAGCCGATTCAGTAACAC+GGG 0.610911 7_2:+87295103 Msa1086260:CDS
TCGGAAATGGAATCCTCGAA+TGG 0.635386 7_2:+87294938 Msa1086260:CDS
AAGCAGCCGATTCAGTAACA+CGG 0.653513 7_2:+87295102 Msa1086260:CDS
TGAGAACGGAGCAAAAGACA+GGG 0.670658 7_2:+87295228 Msa1086260:CDS
CATTTGGAAACATATCTGGG+TGG 0.732935 7_2:+87295305 Msa1086260:CDS
GTGGCATAAAATATATGACG+GGG 0.737363 7_2:+87295324 Msa1086260:CDS
TAATTGTCTCTTGAACATAG+CGG 0.783646 7_2:-87295279 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTCATTATGTTAATAAAAAA+TGG + chr7_2:87295144-87295163 Msa1086260:CDS 15.0%
!!! CTAATTTGTTAAGAATTAAT+CGG - chr7_2:87295511-87295530 None:intergenic 15.0%
!! TATGTTAATAAAAAATGGCT+CGG + chr7_2:87295149-87295168 Msa1086260:CDS 20.0%
!! ATCAACGATTATTACAATAT+CGG - chr7_2:87295354-87295373 None:intergenic 20.0%
! GGAAAACAATTCTTAATTGT+TGG + chr7_2:87295068-87295087 Msa1086260:CDS 25.0%
! TCAACGATTATTACAATATC+GGG - chr7_2:87295353-87295372 None:intergenic 25.0%
!!! ATTAGTTTTTGCAATTTGTG+AGG + chr7_2:87295526-87295545 Msa1086260:CDS 25.0%
!!! TTAGTTTTTGCAATTTGTGA+GGG + chr7_2:87295527-87295546 Msa1086260:CDS 25.0%
TTTATCAGAAGCTTGTGATT+TGG + chr7_2:87295025-87295044 Msa1086260:CDS 30.0%
TAATTGTCTCTTGAACATAG+CGG - chr7_2:87295282-87295301 None:intergenic 30.0%
CAAGAGACAATTATCTCATT+TGG + chr7_2:87295289-87295308 Msa1086260:CDS 30.0%
ATCTCATTTGGAAACATATC+TGG + chr7_2:87295301-87295320 Msa1086260:CDS 30.0%
TCTCATTTGGAAACATATCT+GGG + chr7_2:87295302-87295321 Msa1086260:CDS 30.0%
TGATCAGCAAGAAGAATATA+CGG + chr7_2:87295370-87295389 Msa1086260:CDS 30.0%
!! GTATCGATTAAACAAATCGT+TGG - chr7_2:87295425-87295444 None:intergenic 30.0%
!! TTCATTTTGGCCATGATACT+CGG + chr7_2:87294919-87294938 Msa1086260:CDS 35.0%
! TCGAATGGCACCTTTTATAT+CGG + chr7_2:87294953-87294972 Msa1086260:CDS 35.0%
TTACGCTTTGCCGATATAAA+AGG - chr7_2:87294966-87294985 None:intergenic 35.0%
TTTATATCGGCAAAGCGTAA+AGG + chr7_2:87294966-87294985 Msa1086260:CDS 35.0%
! GTTAATAAAAAATGGCTCGG+AGG + chr7_2:87295152-87295171 Msa1086260:CDS 35.0%
GGGTGGCATAAAATATATGA+CGG + chr7_2:87295322-87295341 Msa1086260:CDS 35.0%
GGTGGCATAAAATATATGAC+GGG + chr7_2:87295323-87295342 Msa1086260:CDS 35.0%
GTGGCATAAAATATATGACG+GGG + chr7_2:87295324-87295343 Msa1086260:CDS 35.0%
TCTTCGAGAATGTATCACTT+TGG + chr7_2:87295394-87295413 Msa1086260:CDS 35.0%
CTTCGAGAATGTATCACTTT+GGG + chr7_2:87295395-87295414 Msa1086260:CDS 35.0%
TCGAAATATCTGCTAGATCT+GGG - chr7_2:87295457-87295476 None:intergenic 35.0%
ATCGAAATATCTGCTAGATC+TGG - chr7_2:87295458-87295477 None:intergenic 35.0%
! ATGGAAGCTGGAGTTCATTT+TGG + chr7_2:87294906-87294925 Msa1086260:CDS 40.0%
GATTCCATTTCCGAGTATCA+TGG - chr7_2:87294932-87294951 None:intergenic 40.0%
!! GATATAAAAGGTGCCATTCG+AGG - chr7_2:87294954-87294973 None:intergenic 40.0%
! GTTTTTGATGCAGCAAGCAT+GGG + chr7_2:87295047-87295066 Msa1086260:CDS 40.0%
! TCGGAGGTATGTTAACGAAT+TGG + chr7_2:87295168-87295187 Msa1086260:CDS 40.0%
AAACGAGACTTCGTAAGTTC+AGG + chr7_2:87295201-87295220 Msa1086260:CDS 40.0%
AACGAGACTTCGTAAGTTCA+GGG + chr7_2:87295202-87295221 Msa1086260:CDS 40.0%
TAAGTTCAGGGACTTGAGAA+CGG + chr7_2:87295214-87295233 Msa1086260:CDS 40.0%
! AACATAGCGGCATCTCTTTT+TGG - chr7_2:87295269-87295288 None:intergenic 40.0%
CATTTGGAAACATATCTGGG+TGG + chr7_2:87295305-87295324 Msa1086260:CDS 40.0%
GCTATAGCATCATCATTAGC+TGG - chr7_2:87295482-87295501 None:intergenic 40.0%
TTGGCCATGATACTCGGAAA+TGG + chr7_2:87294925-87294944 Msa1086260:CDS 45.0%
TCGGAAATGGAATCCTCGAA+TGG + chr7_2:87294938-87294957 Msa1086260:CDS 45.0%
! GGTTTTTGATGCAGCAAGCA+TGG + chr7_2:87295046-87295065 Msa1086260:CDS 45.0%
! AAGCAGCCGATTCAGTAACA+CGG + chr7_2:87295102-87295121 Msa1086260:CDS 45.0%
TTGAGAACGGAGCAAAAGAC+AGG + chr7_2:87295227-87295246 Msa1086260:CDS 45.0%
TGAGAACGGAGCAAAAGACA+GGG + chr7_2:87295228-87295247 Msa1086260:CDS 45.0%
! AGCAGCCGATTCAGTAACAC+GGG + chr7_2:87295103-87295122 Msa1086260:CDS 50.0%
! TGCAGCCCGTGTTACTGAAT+CGG - chr7_2:87295111-87295130 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87294906 87295577 87294906 ID=Msa1086260;Name=Msa1086260
chr7_2 mRNA 87294906 87295577 87294906 ID=Msa1086260-mRNA-1;Parent=Msa1086260;Name=Msa1086260-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|-1|0|1|-1|1|1|0|223
chr7_2 exon 87294906 87295577 87294906 ID=Msa1086260-mRNA-1:exon:23747;Parent=Msa1086260-mRNA-1
chr7_2 CDS 87294906 87295577 87294906 ID=Msa1086260-mRNA-1:cds;Parent=Msa1086260-mRNA-1
Gene Sequence

>Msa1086260

ATGGAAGCTGGAGTTCATTTTGGCCATGATACTCGGAAATGGAATCCTCGAATGGCACCTTTTATATCGGCAAAGCGTAAAGGTATTCATATTACAAATCTTACTCGAACTGCTCGTTTTTTATCAGAAGCTTGTGATTTGGTTTTTGATGCAGCAAGCATGGGAAAACAATTCTTAATTGTTGGTACAAAAAAAAAAGCAGCCGATTCAGTAACACGGGCTGCAATAAGAGCTCGATGTCATTATGTTAATAAAAAATGGCTCGGAGGTATGTTAACGAATTGGTATACTACAGAAACGAGACTTCGTAAGTTCAGGGACTTGAGAACGGAGCAAAAGACAGGGAAACTGAACTCTCTTCCAAAAAGAGATGCCGCTATGTTCAAGAGACAATTATCTCATTTGGAAACATATCTGGGTGGCATAAAATATATGACGGGGTTACCCGATATTGTAATAATCGTTGATCAGCAAGAAGAATATACGGCTCTTCGAGAATGTATCACTTTGGGAATTCCAACGATTTGTTTAATCGATACAAATTGTGACCCAGATCTAGCAGATATTTCGATTCCAGCTAATGATGATGCTATAGCTTCAATCCGATTAATTCTTAACAAATTAGTTTTTGCAATTTGTGAGGGTCGTTCTAGCTATATACGAAATTTTTGA

Protein sequence

>Msa1086260

MEAGVHFGHDTRKWNPRMAPFISAKRKGIHITNLTRTARFLSEACDLVFDAASMGKQFLIVGTKKKAADSVTRAAIRARCHYVNKKWLGGMLTNWYTTETRLRKFRDLRTEQKTGKLNSLPKRDAAMFKRQLSHLETYLGGIKYMTGLPDIVIIVDQQEEYTALRECITLGIPTICLIDTNCDPDLADISIPANDDAIASIRLILNKLVFAICEGRSSYIRNF*