AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene28809

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28809.t1 MTR_7g109510 82.119 151 13 2 1 151 1 137 3.26e-74 218
MS.gene28809.t1 MTR_1g087040 51.370 146 61 3 1 140 1 142 4.07e-39 129
MS.gene28809.t1 MTR_4g070860 48.387 93 47 1 10 101 17 109 1.08e-19 80.5
MS.gene28809.t1 MTR_3g117120 53.012 83 39 0 19 101 27 109 1.13e-19 80.5
MS.gene28809.t1 MTR_1g022495 54.217 83 38 0 19 101 27 109 1.70e-17 74.7
MS.gene28809.t1 MTR_8g086020 40.594 101 55 1 10 105 18 118 8.36e-16 70.5
MS.gene28809.t1 MTR_5g015090 52.857 70 24 1 2 62 32 101 6.42e-13 62.8
MS.gene28809.t1 MTR_4g097440 39.823 113 40 3 7 94 45 154 1.06e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28809.t1 AT3G62420 46.711 152 70 3 1 149 1 144 1.04e-34 118
MS.gene28809.t1 AT2G18160 44.118 102 52 1 18 119 27 123 1.08e-20 83.6
MS.gene28809.t1 AT1G75390 38.849 139 72 3 19 149 38 171 1.44e-20 83.2
MS.gene28809.t1 AT4G34590 48.810 84 43 0 19 102 24 107 1.47e-19 80.1
MS.gene28809.t1 AT1G75390 49.254 67 34 0 19 85 38 104 5.38e-12 59.7

Find 41 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTCCGAATCAAGCGATTA+AGG 0.283521 7.4:-5885556 MS.gene28809:CDS
GGCGATTGTTGGAGAACATT+AGG 0.296251 7.4:-5885779 MS.gene28809:CDS
CAGATTGGTTCTTGCATTGA+TGG 0.301394 7.4:-5885521 None:intergenic
GGTTCAACGTGTGACGAGTT+CGG 0.348908 7.4:-5885949 MS.gene28809:CDS
CACGGGTTCAGTTGCGGATC+TGG 0.352056 7.4:+5885588 None:intergenic
GAGCGATGGACGAGAGAAAA+AGG 0.360427 7.4:-5885908 MS.gene28809:CDS
GTTCAACGTGTGACGAGTTC+GGG 0.369000 7.4:-5885948 MS.gene28809:CDS
TGAATCAATTTGAATGGCTT+CGG 0.385700 7.4:-5885970 None:intergenic
GCGATTGTTGGAGAACATTA+GGG 0.409944 7.4:-5885778 MS.gene28809:CDS
GTGATCGCCGTGCGGATTCA+CGG 0.422997 7.4:+5885868 None:intergenic
AAACGAGAATCGGCGATTGT+TGG 0.446153 7.4:-5885790 MS.gene28809:CDS
AATGCAAACGAAGCCGCTAA+TGG 0.446683 7.4:-5885738 MS.gene28809:CDS
ATCTTCAAGATGAGACAAAC+AGG 0.448219 7.4:-5885818 MS.gene28809:CDS
AACATTAGGGCGAGGGAAGA+AGG 0.454886 7.4:-5885765 MS.gene28809:CDS
ACGTGTGACGAGTTCGGGTT+CGG 0.460336 7.4:-5885943 MS.gene28809:CDS
GACGCCTTAATCGCTTGATT+CGG 0.461919 7.4:+5885552 None:intergenic
AGTTGCGGATCTGGAATCTT+CGG 0.470204 7.4:+5885597 None:intergenic
AGGCGTCTTCGTCTTCAGAT+TGG 0.488511 7.4:-5885536 MS.gene28809:CDS
TGTCCTCGGAGCTCGGATAC+AGG 0.488969 7.4:-5885715 MS.gene28809:CDS
AAAGCTGAGAGGGAAAAGAA+TGG 0.490064 7.4:-5885636 MS.gene28809:CDS
TCGGGTTCGGACGGTGTGAA+TGG 0.491849 7.4:-5885930 MS.gene28809:CDS
GTGAATCCGCACGGCGATCA+CGG 0.512811 7.4:-5885866 MS.gene28809:CDS
CTAATGGTGTCCTCGGAGCT+CGG 0.524737 7.4:-5885722 MS.gene28809:CDS
TGAATCCGCACGGCGATCAC+GGG 0.531059 7.4:-5885865 MS.gene28809:CDS
ACAGGTTGCGAAACGAGAAT+CGG 0.540937 7.4:-5885800 MS.gene28809:CDS
CCGCACGGCGATCACGGGAG+AGG 0.550454 7.4:-5885860 MS.gene28809:CDS
TGTTGGAGAACATTAGGGCG+AGG 0.554484 7.4:-5885773 MS.gene28809:CDS
ATCTGCCACGGGTTCAGTTG+CGG 0.557161 7.4:+5885582 None:intergenic
AGCTCCGAGGACACCATTAG+CGG 0.564090 7.4:+5885725 None:intergenic
GAAGCCGCTAATGGTGTCCT+CGG 0.572523 7.4:-5885729 MS.gene28809:CDS
TCGGACAAAGCATCTGCCAC+GGG 0.574386 7.4:+5885571 None:intergenic
GTTGGAGAACATTAGGGCGA+GGG 0.586730 7.4:-5885772 MS.gene28809:CDS
GGAGAGGAAGCAGAAACTGA+TGG 0.591146 7.4:-5885844 MS.gene28809:CDS
TTCGGACAAAGCATCTGCCA+CGG 0.597740 7.4:+5885570 None:intergenic
GGACGGTGTGAATGGAGCGA+TGG 0.618123 7.4:-5885922 MS.gene28809:CDS
GTGACGAGTTCGGGTTCGGA+CGG 0.621958 7.4:-5885939 MS.gene28809:CDS
CAGATCCGCAACTGAACCCG+TGG 0.634504 7.4:-5885587 MS.gene28809:CDS
TTTCGAACCGTGAATCCGCA+CGG 0.677805 7.4:-5885875 MS.gene28809:CDS
CCTCTCCCGTGATCGCCGTG+CGG 0.684095 7.4:+5885860 None:intergenic
GAGGAAGCAGAAACTGATGG+AGG 0.689697 7.4:-5885841 MS.gene28809:CDS
ATTCCTGTATCCGAGCTCCG+AGG 0.746883 7.4:+5885712 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATCTTCAAGATGAGACAAAC+AGG - chr7.4:5885663-5885682 MS.gene28809:CDS 35.0%
AAAGCTGAGAGGGAAAAGAA+TGG - chr7.4:5885845-5885864 MS.gene28809:CDS 40.0%
GCGATTGTTGGAGAACATTA+GGG - chr7.4:5885703-5885722 MS.gene28809:CDS 40.0%
TGAGAGAGAAAAAGCTGAGA+GGG - chr7.4:5885835-5885854 MS.gene28809:CDS 40.0%
TTGTCCGAATCAAGCGATTA+AGG - chr7.4:5885925-5885944 MS.gene28809:CDS 40.0%
AAACGAGAATCGGCGATTGT+TGG - chr7.4:5885691-5885710 MS.gene28809:CDS 45.0%
AATGCAAACGAAGCCGCTAA+TGG - chr7.4:5885743-5885762 MS.gene28809:CDS 45.0%
ACAGGTTGCGAAACGAGAAT+CGG - chr7.4:5885681-5885700 MS.gene28809:CDS 45.0%
CTGAGAGAGAAAAAGCTGAG+AGG - chr7.4:5885834-5885853 MS.gene28809:CDS 45.0%
GACGCCTTAATCGCTTGATT+CGG + chr7.4:5885932-5885951 None:intergenic 45.0%
GGCGATTGTTGGAGAACATT+AGG - chr7.4:5885702-5885721 MS.gene28809:CDS 45.0%
! AGTTGCGGATCTGGAATCTT+CGG + chr7.4:5885887-5885906 None:intergenic 45.0%
AACATTAGGGCGAGGGAAGA+AGG - chr7.4:5885716-5885735 MS.gene28809:CDS 50.0%
AGGCGTCTTCGTCTTCAGAT+TGG - chr7.4:5885945-5885964 MS.gene28809:CDS 50.0%
GAGCGATGGACGAGAGAAAA+AGG - chr7.4:5885573-5885592 MS.gene28809:CDS 50.0%
GAGGAAGCAGAAACTGATGG+AGG - chr7.4:5885640-5885659 MS.gene28809:CDS 50.0%
GGAGAGGAAGCAGAAACTGA+TGG - chr7.4:5885637-5885656 MS.gene28809:CDS 50.0%
GGTTCAACGTGTGACGAGTT+CGG - chr7.4:5885532-5885551 MS.gene28809:CDS 50.0%
GTTCAACGTGTGACGAGTTC+GGG - chr7.4:5885533-5885552 MS.gene28809:CDS 50.0%
GTTGGAGAACATTAGGGCGA+GGG - chr7.4:5885709-5885728 MS.gene28809:CDS 50.0%
TGTTGGAGAACATTAGGGCG+AGG - chr7.4:5885708-5885727 MS.gene28809:CDS 50.0%
TTTCGAACCGTGAATCCGCA+CGG - chr7.4:5885606-5885625 MS.gene28809:CDS 50.0%
! TTCGGACAAAGCATCTGCCA+CGG + chr7.4:5885914-5885933 None:intergenic 50.0%
AGCTCCGAGGACACCATTAG+CGG + chr7.4:5885759-5885778 None:intergenic 55.0%
ATCTGCCACGGGTTCAGTTG+CGG + chr7.4:5885902-5885921 None:intergenic 55.0%
ATTCCTGTATCCGAGCTCCG+AGG + chr7.4:5885772-5885791 None:intergenic 55.0%
CTAATGGTGTCCTCGGAGCT+CGG - chr7.4:5885759-5885778 MS.gene28809:CDS 55.0%
GAAGCCGCTAATGGTGTCCT+CGG - chr7.4:5885752-5885771 MS.gene28809:CDS 55.0%
! ACGTGTGACGAGTTCGGGTT+CGG - chr7.4:5885538-5885557 MS.gene28809:CDS 55.0%
! TCGGACAAAGCATCTGCCAC+GGG + chr7.4:5885913-5885932 None:intergenic 55.0%
CACGGGTTCAGTTGCGGATC+TGG + chr7.4:5885896-5885915 None:intergenic 60.0%
CAGATCCGCAACTGAACCCG+TGG - chr7.4:5885894-5885913 MS.gene28809:CDS 60.0%
GGACGGTGTGAATGGAGCGA+TGG - chr7.4:5885559-5885578 MS.gene28809:CDS 60.0%
GTGAATCCGCACGGCGATCA+CGG - chr7.4:5885615-5885634 MS.gene28809:CDS 60.0%
GTGATCGCCGTGCGGATTCA+CGG + chr7.4:5885616-5885635 None:intergenic 60.0%
TCGGGTTCGGACGGTGTGAA+TGG - chr7.4:5885551-5885570 MS.gene28809:CDS 60.0%
TGAATCCGCACGGCGATCAC+GGG - chr7.4:5885616-5885635 MS.gene28809:CDS 60.0%
TGTCCTCGGAGCTCGGATAC+AGG - chr7.4:5885766-5885785 MS.gene28809:CDS 60.0%
! GTGACGAGTTCGGGTTCGGA+CGG - chr7.4:5885542-5885561 MS.gene28809:CDS 60.0%
CCTCTCCCGTGATCGCCGTG+CGG + chr7.4:5885624-5885643 None:intergenic 70.0%
CCGCACGGCGATCACGGGAG+AGG - chr7.4:5885621-5885640 MS.gene28809:CDS 75.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 5885524 5885979 5885524 ID=MS.gene28809
chr7.4 mRNA 5885524 5885979 5885524 ID=MS.gene28809.t1;Parent=MS.gene28809
chr7.4 exon 5885524 5885979 5885524 ID=MS.gene28809.t1.exon1;Parent=MS.gene28809.t1
chr7.4 CDS 5885524 5885979 5885524 ID=cds.MS.gene28809.t1;Parent=MS.gene28809.t1
Gene Sequence

>MS.gene28809

ATGGCTTCGGTTCAACGTGTGACGAGTTCGGGTTCGGACGGTGTGAATGGAGCGATGGACGAGAGAAAAAGGAAGAGAATGATTTCGAACCGTGAATCCGCACGGCGATCACGGGAGAGGAAGCAGAAACTGATGGAGGATCTTCAAGATGAGACAAACAGGTTGCGAAACGAGAATCGGCGATTGTTGGAGAACATTAGGGCGAGGGAAGAAGGTTTCAATGCAAACGAAGCCGCTAATGGTGTCCTCGGAGCTCGGATACAGGAATTGACAGATCAATTGAAGTTTCTGAACTCAATCATTGAAAAAGCTGAGAGAGAAAAAGCTGAGAGGGAAAAGAATGGATTTTCTGTTGAGATTCCGAAGATTCCAGATCCGCAACTGAACCCGTGGCAGATGCTTTGTCCGAATCAAGCGATTAAGGCGTCTTCGTCTTCAGATTGGTTCTTGCATTGA
Protein sequence

>MS.gene28809.t1

MASVQRVTSSGSDGVNGAMDERKRKRMISNRESARRSRERKQKLMEDLQDETNRLRNENRRLLENIRAREEGFNANEAANGVLGARIQELTDQLKFLNSIIEKAEREKAEREKNGFSVEIPKIPDPQLNPWQMLCPNQAIKASSSSDWFLH