AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24933

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24933.t1 MTR_0206s0010 92.135 89 7 0 1 89 3 91 3.82e-54 164
MS.gene24933.t1 MTR_4g012950 91.011 89 8 0 1 89 3 91 2.61e-52 159
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24933.t1 AT1G15230 43.697 119 37 2 1 89 3 121 4.21e-18 73.9

Find 33 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATCCTCGCCGGCCGGCTT+TGG 0.289427 4.3:+84380430 None:intergenic
GAGCCGGGAGCTTGTGTTGA+TGG 0.317537 4.3:-84380370 MS.gene24933:CDS
CAGCAAACCTGGTTGTTTCT+CGG 0.368726 4.3:+84380603 None:intergenic
AACGCTTCGTGGATTGATTC+CGG 0.389122 4.3:+84380523 None:intergenic
CTGCTTTGAGAAACGCTTCG+TGG 0.442668 4.3:+84380512 None:intergenic
CGAAGATCCTGCACTTCCAC+CGG 0.490722 4.3:-84380542 MS.gene24933:CDS
ATAATCTGCTGCAGCAAACC+TGG 0.498161 4.3:+84380592 None:intergenic
AGCCGGGAGCTTGTGTTGAT+GGG 0.502950 4.3:-84380369 MS.gene24933:CDS
ATTGATTCCGGTGGAAGTGC+AGG 0.512710 4.3:+84380535 None:intergenic
AGAGCCGGAAAACGAGGAGC+CGG 0.519247 4.3:-84380386 MS.gene24933:CDS
TCGAGAATATTCACATCCTC+CGG 0.535480 4.3:-84380475 MS.gene24933:CDS
GCTTGTGTTGATGGGTTGCA+AGG 0.538167 4.3:-84380361 None:intergenic
GAGCCGGAAAACGAGGAGCC+GGG 0.543615 4.3:-84380385 MS.gene24933:CDS
TATTCTCGATTTCACGGCGG+CGG 0.552490 4.3:+84380489 None:intergenic
CGATCCAAAGCCGGCCGGCG+AGG 0.558176 4.3:-84380434 MS.gene24933:CDS
TGTCGTTGGTGTTATAGAGC+CGG 0.561221 4.3:-84380401 MS.gene24933:CDS
TGTGAATATTCTCGATTTCA+CGG 0.563231 4.3:+84380483 None:intergenic
GACATCTGAAGCATCCTCGC+CGG 0.571070 4.3:+84380420 None:intergenic
GTCGATGCAATCATCTTCGC+CGG 0.571440 4.3:+84380456 None:intergenic
GAGTCCACCGAGAAACAACC+AGG 0.578103 4.3:-84380610 MS.gene24933:CDS
TTGCATCGACGATCCAAAGC+CGG 0.583740 4.3:-84380443 MS.gene24933:CDS
AACCCATCAACACAAGCTCC+CGG 0.588157 4.3:+84380367 None:intergenic
ATCGACGATCCAAAGCCGGC+CGG 0.592029 4.3:-84380439 MS.gene24933:CDS
TCTGAAGCATCCTCGCCGGC+CGG 0.595069 4.3:+84380424 None:intergenic
GAGGATGCTTCAGATGTCGT+TGG 0.615781 4.3:-84380415 MS.gene24933:CDS
TGTTATAGAGCCGGAAAACG+AGG 0.616666 4.3:-84380392 MS.gene24933:CDS
CAAACCTGGTTGTTTCTCGG+TGG 0.627408 4.3:+84380606 None:intergenic
GCTTCGTGGATTGATTCCGG+TGG 0.647677 4.3:+84380526 None:intergenic
GATGCAATCATCTTCGCCGG+AGG 0.648234 4.3:+84380459 None:intergenic
AGACCTGCGTCTTCTAGACG+CGG 0.716883 4.3:+84380565 None:intergenic
CCTGCGTCTTCTAGACGCGG+TGG 0.721425 4.3:+84380568 None:intergenic
CCACCGCGTCTAGAAGACGC+AGG 0.752546 4.3:-84380568 MS.gene24933:CDS
GAATATTCTCGATTTCACGG+CGG 0.800990 4.3:+84380486 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGTGAATATTCTCGATTTCA+CGG + chr4.3:84380489-84380508 None:intergenic 30.0%
GAATATTCTCGATTTCACGG+CGG + chr4.3:84380486-84380505 None:intergenic 40.0%
TCGAGAATATTCACATCCTC+CGG - chr4.3:84380494-84380513 MS.gene24933:CDS 40.0%
ATAATCTGCTGCAGCAAACC+TGG + chr4.3:84380380-84380399 None:intergenic 45.0%
TGTTATAGAGCCGGAAAACG+AGG - chr4.3:84380577-84380596 MS.gene24933:CDS 45.0%
! AACGCTTCGTGGATTGATTC+CGG + chr4.3:84380449-84380468 None:intergenic 45.0%
!! CAGCAAACCTGGTTGTTTCT+CGG + chr4.3:84380369-84380388 None:intergenic 45.0%
!! TGTCGTTGGTGTTATAGAGC+CGG - chr4.3:84380568-84380587 MS.gene24933:CDS 45.0%
AACCCATCAACACAAGCTCC+CGG + chr4.3:84380605-84380624 None:intergenic 50.0%
GAGGATGCTTCAGATGTCGT+TGG - chr4.3:84380554-84380573 MS.gene24933:CDS 50.0%
GTCGATGCAATCATCTTCGC+CGG + chr4.3:84380516-84380535 None:intergenic 50.0%
TATTCTCGATTTCACGGCGG+CGG + chr4.3:84380483-84380502 None:intergenic 50.0%
! ATTGATTCCGGTGGAAGTGC+AGG + chr4.3:84380437-84380456 None:intergenic 50.0%
! TTGCATCGACGATCCAAAGC+CGG - chr4.3:84380526-84380545 MS.gene24933:CDS 50.0%
!! CAAACCTGGTTGTTTCTCGG+TGG + chr4.3:84380366-84380385 None:intergenic 50.0%
!! CTGCTTTGAGAAACGCTTCG+TGG + chr4.3:84380460-84380479 None:intergenic 50.0%
AGACCTGCGTCTTCTAGACG+CGG + chr4.3:84380407-84380426 None:intergenic 55.0%
CGAAGATCCTGCACTTCCAC+CGG - chr4.3:84380427-84380446 MS.gene24933:CDS 55.0%
GATGCAATCATCTTCGCCGG+AGG + chr4.3:84380513-84380532 None:intergenic 55.0%
! AGCCGGGAGCTTGTGTTGAT+GGG - chr4.3:84380600-84380619 MS.gene24933:CDS 55.0%
! GACATCTGAAGCATCCTCGC+CGG + chr4.3:84380552-84380571 None:intergenic 55.0%
! GCTTCGTGGATTGATTCCGG+TGG + chr4.3:84380446-84380465 None:intergenic 55.0%
AGAGCCGGAAAACGAGGAGC+CGG - chr4.3:84380583-84380602 MS.gene24933:CDS 60.0%
ATCGACGATCCAAAGCCGGC+CGG - chr4.3:84380530-84380549 MS.gene24933:CDS 60.0%
GAGCCGGGAGCTTGTGTTGA+TGG - chr4.3:84380599-84380618 MS.gene24933:CDS 60.0%
CCACCGCGTCTAGAAGACGC+AGG - chr4.3:84380401-84380420 MS.gene24933:CDS 65.0%
CCTGCGTCTTCTAGACGCGG+TGG + chr4.3:84380404-84380423 None:intergenic 65.0%
GAGCCGGAAAACGAGGAGCC+GGG - chr4.3:84380584-84380603 MS.gene24933:CDS 65.0%
! GCTCCCGGCTCCTCGTTTTC+CGG + chr4.3:84380590-84380609 None:intergenic 65.0%
! TCTGAAGCATCCTCGCCGGC+CGG + chr4.3:84380548-84380567 None:intergenic 65.0%
CGATCCAAAGCCGGCCGGCG+AGG - chr4.3:84380535-84380554 MS.gene24933:CDS 75.0%
! GCATCCTCGCCGGCCGGCTT+TGG + chr4.3:84380542-84380561 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 84380362 84380629 84380362 ID=MS.gene24933
chr4.3 mRNA 84380362 84380629 84380362 ID=MS.gene24933.t1;Parent=MS.gene24933
chr4.3 exon 84380362 84380629 84380362 ID=MS.gene24933.t1.exon1;Parent=MS.gene24933.t1
chr4.3 CDS 84380362 84380629 84380362 ID=cds.MS.gene24933.t1;Parent=MS.gene24933.t1
Gene Sequence

>MS.gene24933

TCCACCGAGAAACAACCAGGTTTGCTGCAGCAGATTATACCACCGCGTCTAGAAGACGCAGGTCTCGAAGATCCTGCACTTCCACCGGAATCAATCCACGAAGCGTTTCTCAAAGCAGCCGCCGCCGTGAAATCGAGAATATTCACATCCTCCGGCGAAGATGATTGCATCGACGATCCAAAGCCGGCCGGCGAGGATGCTTCAGATGTCGTTGGTGTTATAGAGCCGGAAAACGAGGAGCCGGGAGCTTGTGTTGATGGGTTGCAAG
Protein sequence

>MS.gene24933.t1

STEKQPGLLQQIIPPRLEDAGLEDPALPPESIHEAFLKAAAAVKSRIFTSSGEDDCIDDPKPAGEDASDVVGVIEPENEEPGACVDGLQ