AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene75763

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75763.t1 MTR_3g109420 100.000 46 0 0 1 46 1 46 2.61e-27 97.4
MS.gene75763.t1 MTR_3g109420 82.500 40 6 1 39 78 132 170 2.82e-18 74.3
MS.gene75763.t1 MTR_1g008700 84.783 46 7 0 1 46 1 46 1.73e-22 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75763.t1 AT4G32690 73.913 46 12 0 1 46 1 46 7.77e-17 70.9

Find 16 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATAGAACCTGTTGTAGAAAT+TGG 0.299176 3.3:+90046053 None:intergenic
TTTCCACCAATTTCTACAAC+AGG 0.420675 3.3:-90046059 MS.gene75763:intron
CTTCCAGCTGCATCCTTGCA+AGG 0.423236 3.3:+90045112 None:intergenic
AAACAAGTTGGTGTCATCAA+TGG 0.436122 3.3:+90046113 None:intergenic
AAAGGTTAATGAAAGTTTGA+AGG 0.487596 3.3:+90046079 None:intergenic
TTCCAGCTGCATCCTTGCAA+GGG 0.503260 3.3:+90045113 None:intergenic
CACCCTTGCAAGGATGCAGC+TGG 0.514180 3.3:-90045115 MS.gene75763:CDS
TGTTGTAGAAATTGGTGGAA+AGG 0.527682 3.3:+90046061 None:intergenic
CTGCATCCTTGCAAGGGTGA+AGG 0.528329 3.3:+90045119 None:intergenic
TGCAAGAGAAGGCTTCTGAA+TGG 0.530466 3.3:-90046164 MS.gene75763:CDS
GAACCTGTTGTAGAAATTGG+TGG 0.539038 3.3:+90046056 None:intergenic
TCAAAGCCTTCACCCTTGCA+AGG 0.595706 3.3:-90045125 MS.gene75763:CDS
ACCAACTTGTTTCAAAAGCT+AGG 0.598000 3.3:-90046102 MS.gene75763:CDS
CTTGCAAGGATGCAGCTGGA+AGG 0.604226 3.3:-90045111 MS.gene75763:CDS
GATGCAGAATCTGCAAGAGA+AGG 0.605698 3.3:-90046175 MS.gene75763:CDS
GAGAAGGCTTCTGAATGGAG+TGG 0.664521 3.3:-90046159 MS.gene75763:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTCAATAATATTCTTTATT+TGG - chr3.3:90045692-90045711 MS.gene75763:intron 15.0%
!! TATATGACCTAAATATATAT+AGG + chr3.3:90045794-90045813 None:intergenic 15.0%
!!! CTTTTAGATTTTTAACTTTT+CGG - chr3.3:90045489-90045508 MS.gene75763:intron 15.0%
!!! GTCAATAATATTCTTTATTT+GGG - chr3.3:90045693-90045712 MS.gene75763:intron 15.0%
!!! TCAATAATATTCTTTATTTG+GGG - chr3.3:90045694-90045713 MS.gene75763:intron 15.0%
!!! TTTGAAACCTATATATATTT+AGG - chr3.3:90045784-90045803 MS.gene75763:intron 15.0%
!! AAAGTTAATCAACATTATCT+TGG + chr3.3:90045988-90046007 None:intergenic 20.0%
!! ATATATCTCTAATAAATGTG+TGG - chr3.3:90045811-90045830 MS.gene75763:intron 20.0%
! AAAGGTTAATGAAAGTTTGA+AGG + chr3.3:90045188-90045207 None:intergenic 25.0%
! ACTAAGTTCATGACAATTAA+TGG - chr3.3:90045277-90045296 MS.gene75763:intron 25.0%
! ATATATAGGTTTCAAAGCTT+AGG + chr3.3:90045780-90045799 None:intergenic 25.0%
!! TAATATTCTTTATTTGGGGA+TGG - chr3.3:90045698-90045717 MS.gene75763:intron 25.0%
!!! AACCTGTGTTTTTACTTTTT+AGG - chr3.3:90046075-90046094 MS.gene75763:CDS 25.0%
ATAGAACCTGTTGTAGAAAT+TGG + chr3.3:90045214-90045233 None:intergenic 30.0%
GTCATGAACTTAGTAAAGAA+AGG + chr3.3:90045271-90045290 None:intergenic 30.0%
TGCCTAAAAAGTAAAAACAC+AGG + chr3.3:90046080-90046099 None:intergenic 30.0%
! TTGATTCTTCTTTTCAACTC+CGG + chr3.3:90046123-90046142 None:intergenic 30.0%
ACTTCATATGCAACAAGCAT+TGG - chr3.3:90045935-90045954 MS.gene75763:intron 35.0%
ATGTCCTGTAATGTGAAGTA+CGG + chr3.3:90045853-90045872 None:intergenic 35.0%
TCAAAACCAGTACGAATTCT+TGG - chr3.3:90045379-90045398 MS.gene75763:intron 35.0%
TGCTTTGTCTTTATCAGACT+TGG + chr3.3:90045357-90045376 None:intergenic 35.0%
TGTTGTAGAAATTGGTGGAA+AGG + chr3.3:90045206-90045225 None:intergenic 35.0%
TTTCCACCAATTTCTACAAC+AGG - chr3.3:90045205-90045224 MS.gene75763:intron 35.0%
! ACCAACTTGTTTCAAAAGCT+AGG - chr3.3:90045162-90045181 MS.gene75763:CDS 35.0%
! ACTGCATATTTTCTTGTTGC+CGG - chr3.3:90046101-90046120 MS.gene75763:CDS 35.0%
!! AAACAAGTTGGTGTCATCAA+TGG + chr3.3:90045154-90045173 None:intergenic 35.0%
CATATGAAGTAACCACCTCT+CGG + chr3.3:90045925-90045944 None:intergenic 40.0%
CGATGTCTAGTAATTAGAGC+AGG + chr3.3:90045876-90045895 None:intergenic 40.0%
GAACCTGTTGTAGAAATTGG+TGG + chr3.3:90045211-90045230 None:intergenic 40.0%
GAATTCTTGGTCCAGAGAAT+GGG - chr3.3:90045392-90045411 MS.gene75763:intron 40.0%
GGGATGGTTAGTAAAATGAC+AGG - chr3.3:90045714-90045733 MS.gene75763:intron 40.0%
!!! GCCTAGCTTTTGAAACAAGT+TGG + chr3.3:90045166-90045185 None:intergenic 40.0%
CCTCTGTATTCTCAGAGAAG+AGG - chr3.3:90045422-90045441 MS.gene75763:intron 45.0%
CGAATTCTTGGTCCAGAGAA+TGG - chr3.3:90045391-90045410 MS.gene75763:intron 45.0%
GCTACCGTACTTCACATTAC+AGG - chr3.3:90045846-90045865 MS.gene75763:intron 45.0%
GCTTCATGTGTCACAGGAAA+TGG + chr3.3:90045900-90045919 None:intergenic 45.0%
TCTGGACCAAGAATTCGTAC+TGG + chr3.3:90045388-90045407 None:intergenic 45.0%
TGCAAGAGAAGGCTTCTGAA+TGG - chr3.3:90045100-90045119 MS.gene75763:CDS 45.0%
! CCTCTTCTCTGAGAATACAG+AGG + chr3.3:90045425-90045444 None:intergenic 45.0%
! CTTCTCTGAGAATACAGAGG+AGG + chr3.3:90045422-90045441 None:intergenic 45.0%
! GTGTATGATGACGATGAGAG+TGG - chr3.3:90045315-90045334 MS.gene75763:intron 45.0%
! TGATGACGATGAGAGTGGTT+TGG - chr3.3:90045320-90045339 MS.gene75763:intron 45.0%
GAGAAGGCTTCTGAATGGAG+TGG - chr3.3:90045105-90045124 MS.gene75763:CDS 50.0%
TCAAAGCCTTCACCCTTGCA+AGG - chr3.3:90046139-90046158 MS.gene75763:CDS 50.0%
TTCCAGCTGCATCCTTGCAA+GGG + chr3.3:90046154-90046173 None:intergenic 50.0%
TTCTTGGTCCAGAGAATGGG+AGG - chr3.3:90045395-90045414 MS.gene75763:intron 50.0%
CTGCATCCTTGCAAGGGTGA+AGG + chr3.3:90046148-90046167 None:intergenic 55.0%
CTTCCAGCTGCATCCTTGCA+AGG + chr3.3:90046155-90046174 None:intergenic 55.0%
CTTGCAAGGATGCAGCTGGA+AGG - chr3.3:90046153-90046172 MS.gene75763:CDS 55.0%
TCGGCAGCTTCATGTGTCAC+AGG + chr3.3:90045906-90045925 None:intergenic 55.0%
TGACACATGAAGCTGCCGAG+AGG - chr3.3:90045907-90045926 MS.gene75763:intron 55.0%
CACATGAAGCTGCCGAGAGG+TGG - chr3.3:90045910-90045929 MS.gene75763:intron 60.0%
CACCCTTGCAAGGATGCAGC+TGG - chr3.3:90046149-90046168 MS.gene75763:CDS 60.0%
GAGGAGGACCTCCCATTCTC+TGG + chr3.3:90045406-90045425 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 90045090 90046196 90045090 ID=MS.gene75763
chr3.3 mRNA 90045090 90046196 90045090 ID=MS.gene75763.t1;Parent=MS.gene75763
chr3.3 exon 90046060 90046196 90046060 ID=MS.gene75763.t1.exon1;Parent=MS.gene75763.t1
chr3.3 CDS 90046060 90046196 90046060 ID=cds.MS.gene75763.t1;Parent=MS.gene75763.t1
chr3.3 exon 90045090 90045189 90045090 ID=MS.gene75763.t1.exon2;Parent=MS.gene75763.t1
chr3.3 CDS 90045090 90045189 90045090 ID=cds.MS.gene75763.t1;Parent=MS.gene75763.t1
Gene Sequence

>MS.gene75763

ATGCAGAATCTGCAAGAGAAGGCTTCTGAATGGAGTGGTGTTGAGACAAATCATGCTTTTGCCATTGATGACACCAACTTGTTTCAAAAGCTAGGCCTTCAAACTTTCATTAACCTTTCCACCAATTTCTACAACAGGTTCTATATATATTCAACTTATATATTTCAATATTAAATAACCTTTCTTTACTAAGTTCATGACAATTAATGGTTGTGCTATAATAGAGTGTATGATGACGATGAGAGTGGTTTGGTTCAATATTTGCCAAGTCTGATAAAGACAAAGCAATTCAAAACCAGTACGAATTCTTGGTCCAGAGAATGGGAGGTCCTCCTCTGTATTCTCAGAGAAGAGGTCAATATTCTTTATTTTATTTTTATTTCACTTTTCATAGAAACACTTTTAGATTTTTAACTTTTCGGAAAAATACTTCTAATTAGTGATTACTATTTTACTGATTTTTTTGTACTCAAGTAAGCAAACAATATGATAGATTTTTTTCAAAAAATAAATAAATACTATTATAGATATATTTTGAAAAATGCTATTAATTCTTGATTAATTTAACACTACTAACAATTTTTTTTTAGTGTATGTGATTTAGTCAATAATATTCTTTATTTGGGGATGGTTAGTAAAATGACAGGTTTTGAACTTACTACACAATGAGTTTATAAGTGATTATTGCCTAAGCTTTGAAACCTATATATATTTAGGTCATATATATCTCTAATAAATGTGTGGCTTAGTTCATTTGCTACCGTACTTCACATTACAGGACATCCTGCTCTAATTACTAGACATCGACCATTTCCTGTGACACATGAAGCTGCCGAGAGGTGGTTACTTCATATGCAACAAGCATTGGACAATATTTCAGATATAGATCATGATTCCAAGATAATGTTGATTAACTTTTTCAGATTTATTATCTTCACTTTGCAGAAATCAAATCAATAAAAATAAATAATGTTCATGATATAACAACCTGTGTTTTTACTTTTTAGGCACACTGCATATTTTCTTGTTGCCGGAGTTGAAAAGAAGAATCAAAGCCTTCACCCTTGCAAGGATGCAGCTGGAAGGCATCCATGTAAAAACTTTTAA
Protein sequence

>MS.gene75763.t1

MQNLQEKASEWSGVETNHAFAIDDTNLFQKLGLQTFINLSTNFYNRHTAYFLVAGVEKKNQSLHPCKDAAGRHPCKNF