AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene03294


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03294.t1 MTR_0856s0010 40.940 149 85 2 16 163 4 150 9.92e-32 111
MS.gene03294.t1 MTR_1g019850 30.137 146 90 5 20 159 41 180 2.64e-14 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTGTTGATGTTTCGGATTC+CGG 0.181586 6.2:-30446466 MS.gene03294:CDS
GATCGCAAACCCTTGTTTCA+TGG 0.299904 6.2:+30446339 None:intergenic
GTGTTGATGTTTCGGATTCC+GGG 0.331005 6.2:-30446465 MS.gene03294:CDS
TTGCTTTAAAGAAGGGTCTA+TGG 0.361166 6.2:-30446168 MS.gene03294:CDS
TGCTGCTCGTGTTGATGTTT+CGG 0.374211 6.2:-30446473 MS.gene03294:CDS
TATCGGTATGTCTATTAAAT+CGG 0.409891 6.2:-30446395 MS.gene03294:CDS
TCTCCATCAGGGGCTAATAA+AGG 0.410771 6.2:+30446508 None:intergenic
GCAAACAATCGTGATTTACT+TGG 0.414132 6.2:+30446103 None:intergenic
AAAGGATGATCGATCAATAT+AGG 0.415391 6.2:+30446526 None:intergenic
AGTAAATCACGATTGTTTGC+TGG 0.430968 6.2:-30446100 MS.gene03294:CDS
AAAACTAGAAACTCTAAGAA+AGG 0.460549 6.2:-30446316 MS.gene03294:CDS
TTAATAGACATACCGATAGT+AGG 0.461742 6.2:+30446400 None:intergenic
GATAACGGTTGCTTTAAAGA+AGG 0.473052 6.2:-30446176 MS.gene03294:CDS
GAGCAATCAAGTTTCTTCGT+TGG 0.480101 6.2:+30446205 None:intergenic
CCGTCATCTAGCTCTCCATC+AGG 0.480197 6.2:+30446496 None:intergenic
ATTTGTTGTTTCAAAGGTCC+CGG 0.485747 6.2:+30446447 None:intergenic
GACAGCATTTGTTGTTTCAA+AGG 0.491833 6.2:+30446441 None:intergenic
CTTGTTTCATGGCATATTCA+CGG 0.492232 6.2:+30446350 None:intergenic
CGTGAATATGCCATGAAACA+AGG 0.498225 6.2:-30446349 MS.gene03294:CDS
GTTGGATTCGTCTTCAAAGT+TGG 0.502236 6.2:+30446223 None:intergenic
CACTTATGCTCGATGGCTGA+CGG 0.509764 6.2:-30446553 None:intergenic
ATAACGGTTGCTTTAAAGAA+GGG 0.522275 6.2:-30446175 MS.gene03294:CDS
AAACTAGAAACTCTAAGAAA+GGG 0.523644 6.2:-30446315 MS.gene03294:CDS
CGTCATCTAGCTCTCCATCA+GGG 0.529370 6.2:+30446497 None:intergenic
GGATTCGTCTTCAAAGTTGG+TGG 0.530111 6.2:+30446226 None:intergenic
CATCCTTTATTAGCCCCTGA+TGG 0.541554 6.2:-30446511 MS.gene03294:CDS
AACTCTAAGAAAGGGTCAGA+TGG 0.545893 6.2:-30446307 MS.gene03294:CDS
TTGGTGGTATGTTTGATTCG+TGG 0.550924 6.2:+30446242 None:intergenic
TGATTGCTCAGCTAAGATAA+CGG 0.550952 6.2:-30446191 MS.gene03294:CDS
ATTCTAACTTGTGCAAGAGA+AGG 0.552020 6.2:-30446268 MS.gene03294:CDS
GATGAATTCACGCCTACTAT+CGG 0.575926 6.2:-30446412 MS.gene03294:CDS
GTGAATATGCCATGAAACAA+GGG 0.602322 6.2:-30446348 MS.gene03294:CDS
GTCATCTAGCTCTCCATCAG+GGG 0.623144 6.2:+30446498 None:intergenic
AGATTGATATGCATGCATAG+TGG 0.627055 6.2:-30446069 None:intergenic
GGATGATCGATCAATATAGG+AGG 0.639611 6.2:+30446529 None:intergenic
CCTGATGGAGAGCTAGATGA+CGG 0.653770 6.2:-30446496 MS.gene03294:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TATCGGTATGTCTATTAAAT+CGG - chr6.2:30446218-30446237 MS.gene03294:CDS 25.0%
!! AAAACTAGAAACTCTAAGAA+AGG - chr6.2:30446297-30446316 MS.gene03294:CDS 25.0%
!! AAACTAGAAACTCTAAGAAA+GGG - chr6.2:30446298-30446317 MS.gene03294:CDS 25.0%
AAAGGATGATCGATCAATAT+AGG + chr6.2:30446090-30446109 None:intergenic 30.0%
TTAATAGACATACCGATAGT+AGG + chr6.2:30446216-30446235 None:intergenic 30.0%
!! ATAACGGTTGCTTTAAAGAA+GGG - chr6.2:30446438-30446457 MS.gene03294:CDS 30.0%
AGTAAATCACGATTGTTTGC+TGG - chr6.2:30446513-30446532 MS.gene03294:CDS 35.0%
CTTGTTTCATGGCATATTCA+CGG + chr6.2:30446266-30446285 None:intergenic 35.0%
GCAAACAATCGTGATTTACT+TGG + chr6.2:30446513-30446532 None:intergenic 35.0%
GTGAATATGCCATGAAACAA+GGG - chr6.2:30446265-30446284 MS.gene03294:CDS 35.0%
TGATTGCTCAGCTAAGATAA+CGG - chr6.2:30446422-30446441 MS.gene03294:CDS 35.0%
! ATTCTAACTTGTGCAAGAGA+AGG - chr6.2:30446345-30446364 MS.gene03294:CDS 35.0%
!! ATTTGTTGTTTCAAAGGTCC+CGG + chr6.2:30446169-30446188 None:intergenic 35.0%
!! GACAGCATTTGTTGTTTCAA+AGG + chr6.2:30446175-30446194 None:intergenic 35.0%
!! GATAACGGTTGCTTTAAAGA+AGG - chr6.2:30446437-30446456 MS.gene03294:CDS 35.0%
!! TTGCTTTAAAGAAGGGTCTA+TGG - chr6.2:30446445-30446464 MS.gene03294:CDS 35.0%
CGTGAATATGCCATGAAACA+AGG - chr6.2:30446264-30446283 MS.gene03294:CDS 40.0%
GAGCAATCAAGTTTCTTCGT+TGG + chr6.2:30446411-30446430 None:intergenic 40.0%
GATGAATTCACGCCTACTAT+CGG - chr6.2:30446201-30446220 MS.gene03294:CDS 40.0%
GGATGATCGATCAATATAGG+AGG + chr6.2:30446087-30446106 None:intergenic 40.0%
GTTGGATTCGTCTTCAAAGT+TGG + chr6.2:30446393-30446412 None:intergenic 40.0%
! AACTCTAAGAAAGGGTCAGA+TGG - chr6.2:30446306-30446325 MS.gene03294:CDS 40.0%
! TTGGTGGTATGTTTGATTCG+TGG + chr6.2:30446374-30446393 None:intergenic 40.0%
CATCCTTTATTAGCCCCTGA+TGG - chr6.2:30446102-30446121 MS.gene03294:CDS 45.0%
GGATTCGTCTTCAAAGTTGG+TGG + chr6.2:30446390-30446409 None:intergenic 45.0%
TCTCCATCAGGGGCTAATAA+AGG + chr6.2:30446108-30446127 None:intergenic 45.0%
! CGTGTTGATGTTTCGGATTC+CGG - chr6.2:30446147-30446166 MS.gene03294:CDS 45.0%
! GATCGCAAACCCTTGTTTCA+TGG + chr6.2:30446277-30446296 None:intergenic 45.0%
! GTGTTGATGTTTCGGATTCC+GGG - chr6.2:30446148-30446167 MS.gene03294:CDS 45.0%
! TGCTGCTCGTGTTGATGTTT+CGG - chr6.2:30446140-30446159 MS.gene03294:CDS 45.0%
CCTGATGGAGAGCTAGATGA+CGG - chr6.2:30446117-30446136 MS.gene03294:CDS 50.0%
!! CGTCATCTAGCTCTCCATCA+GGG + chr6.2:30446119-30446138 None:intergenic 50.0%
!! GTCATCTAGCTCTCCATCAG+GGG + chr6.2:30446118-30446137 None:intergenic 50.0%
!! CCGTCATCTAGCTCTCCATC+AGG + chr6.2:30446120-30446139 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 30446072 30446563 30446072 ID=MS.gene03294
chr6.2 mRNA 30446072 30446563 30446072 ID=MS.gene03294.t1;Parent=MS.gene03294
chr6.2 exon 30446072 30446563 30446072 ID=MS.gene03294.t1.exon1;Parent=MS.gene03294.t1
chr6.2 CDS 30446072 30446563 30446072 ID=cds.MS.gene03294.t1;Parent=MS.gene03294.t1
Gene Sequence

>MS.gene03294

ATGGCTGACGGTCCTCCTATATTGATCGATCATCCTTTATTAGCCCCTGATGGAGAGCTAGATGACGGTGCTGCTCGTGTTGATGTTTCGGATTCCGGGACCTTTGAAACAACAAATGCTGTCGCAACAGATGAATTCACGCCTACTATCGGTATGTCTATTAAATCGGTTGCAGATTGTAAGTCTTTTTACCGTGAATATGCCATGAAACAAGGGTTTGCGATCAAAACTAGAAACTCTAAGAAAGGGTCAGATGGCATGTTAAGATATTTCATTCTAACTTGTGCAAGAGAAGGTCACCACGAATCAAACATACCACCAACTTTGAAGACGAATCCAACGAAGAAACTTGATTGCTCAGCTAAGATAACGGTTGCTTTAAAGAAGGGTCTATGGACTATTTTGTCATTTAATTCATGTCATAATCATGAGATAAGTCCAAGTAAATCACGATTGTTTGCTGGCAATAAGAAGATTGATATGCATGCATAG

Protein sequence

>MS.gene03294.t1

MADGPPILIDHPLLAPDGELDDGAARVDVSDSGTFETTNAVATDEFTPTIGMSIKSVADCKSFYREYAMKQGFAIKTRNSKKGSDGMLRYFILTCAREGHHESNIPPTLKTNPTKKLDCSAKITVALKKGLWTILSFNSCHNHEISPSKSRLFAGNKKIDMHA