AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene58575

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene58575.t1 MTR_5g036820 92.593 81 6 0 1 81 6 86 7.47e-52 157
MS.gene58575.t1 MTR_5g036790 62.195 82 29 1 1 82 6 85 9.77e-32 106
MS.gene58575.t1 MTR_7g013525 40.964 83 46 2 1 82 1 81 5.65e-16 66.2
MS.gene58575.t1 MTR_6g008995 46.377 69 35 1 11 79 117 183 4.05e-14 65.9
MS.gene58575.t1 MTR_6g008995 46.377 69 35 1 11 79 60 126 4.34e-14 65.9
MS.gene58575.t1 MTR_6g008970 43.056 72 39 1 8 79 142 211 2.05e-13 63.9
MS.gene58575.t1 MTR_5g036670 42.029 69 38 1 11 79 125 191 7.09e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene58575.t1 AT3G01320 48.387 62 30 1 18 79 60 119 1.05e-11 58.9
MS.gene58575.t1 AT3G01320 38.889 72 42 1 8 79 135 204 2.48e-11 58.2
MS.gene58575.t1 AT3G01320 48.387 62 30 1 18 79 60 119 1.07e-11 58.9
MS.gene58575.t1 AT3G01320 38.889 72 42 1 8 79 135 204 2.44e-11 58.2
MS.gene58575.t1 AT5G15020 40.278 72 41 1 8 79 129 198 1.85e-11 58.5
MS.gene58575.t1 AT5G15020 40.278 72 41 1 8 79 129 198 1.98e-11 58.2

Find 15 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGCTATGTGCGCGAGGTGA+AGG 0.474033 5.3:-25020200 MS.gene58575:intron
GGCCATGATGACCTCATTGA+TGG 0.490730 5.3:-25019641 MS.gene58575:CDS
TGAAAAGAATTTACGCTGAC+CGG 0.518590 5.3:-25020249 MS.gene58575:CDS
ACCCATCAATGAGGTCATCA+TGG 0.540419 5.3:+25019639 None:intergenic
TTACGCTGACCGGCCAGTGG+TGG 0.569040 5.3:-25020239 MS.gene58575:CDS
TGTTGGTAATGTTATTAGTG+AGG 0.580980 5.3:-25020000 MS.gene58575:intron
ATAGAAAGAGAAAAGACTGT+TGG 0.583807 5.3:-25020017 MS.gene58575:CDS
GCCATGATGACCTCATTGAT+GGG 0.591592 5.3:-25019640 MS.gene58575:CDS
ACTGATAATCCACCACTGGC+CGG 0.602964 5.3:+25020230 None:intergenic
ATATACTGATAATCCACCAC+TGG 0.603993 5.3:+25020226 None:intergenic
AATTTACGCTGACCGGCCAG+TGG 0.644697 5.3:-25020242 MS.gene58575:CDS
ACAAATTTCATTCCTCTACG+TGG 0.649296 5.3:-25019614 MS.gene58575:CDS
CATATACACTAGCCACGTAG+AGG 0.658315 5.3:+25019602 None:intergenic
AATTTGTAAACCCATCAATG+AGG 0.691671 5.3:+25019630 None:intergenic
TATTTCGAGCTATGTGCGCG+AGG 0.697429 5.3:-25020206 MS.gene58575:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAAAATAATATTTTTAT+TGG - chr5.3:25019967-25019986 MS.gene58575:intron 0.0%
!! CATGAAAAAAAATATCTATT+AGG + chr5.3:25019754-25019773 None:intergenic 15.0%
!! AAAAAACAATAGTGTGAAAT+AGG - chr5.3:25019992-25020011 MS.gene58575:intron 20.0%
!! AAAAACAATAGTGTGAAATA+GGG - chr5.3:25019993-25020012 MS.gene58575:intron 20.0%
!! AAGAGGAAAGAAAAATAAAA+AGG + chr5.3:25020143-25020162 None:intergenic 20.0%
!! TAAAAATTGTTTATGTCATG+TGG - chr5.3:25020041-25020060 MS.gene58575:CDS 20.0%
!! TATATGTAATTGTAGTTTAG+AGG + chr5.3:25020118-25020137 None:intergenic 20.0%
!!! AATTATGATTTTACTTCTTC+AGG - chr5.3:25020179-25020198 MS.gene58575:intron 20.0%
!!! TGATAGCAATAGTATTTTTA+TGG + chr5.3:25020087-25020106 None:intergenic 20.0%
! TAAAATGAGTATTACACAAG+AGG + chr5.3:25020160-25020179 None:intergenic 25.0%
!! TGTTGTTTAATTATGTCATG+TGG - chr5.3:25019887-25019906 MS.gene58575:intron 25.0%
AATTTGTAAACCCATCAATG+AGG + chr5.3:25020233-25020252 None:intergenic 30.0%
ATAGAAAGAGAAAAGACTGT+TGG - chr5.3:25019843-25019862 MS.gene58575:intron 30.0%
GGTGAAGGTAAGTTATATTA+TGG - chr5.3:25019675-25019694 MS.gene58575:intron 30.0%
TGTGGTCACAATTATAATTG+AGG - chr5.3:25019905-25019924 MS.gene58575:intron 30.0%
!! TGTTGGTAATGTTATTAGTG+AGG - chr5.3:25019860-25019879 MS.gene58575:intron 30.0%
ACAAATTTCATTCCTCTACG+TGG - chr5.3:25020246-25020265 MS.gene58575:CDS 35.0%
ATATACTGATAATCCACCAC+TGG + chr5.3:25019637-25019656 None:intergenic 35.0%
GAGGCATAGTGAAATGATAT+TGG - chr5.3:25019924-25019943 MS.gene58575:intron 35.0%
TGAAAAGAATTTACGCTGAC+CGG - chr5.3:25019611-25019630 MS.gene58575:CDS 35.0%
ACCCATCAATGAGGTCATCA+TGG + chr5.3:25020224-25020243 None:intergenic 45.0%
GCCATGATGACCTCATTGAT+GGG - chr5.3:25020220-25020239 MS.gene58575:CDS 45.0%
! CAGGTTGCTGAGCTTTTTGA+AGG - chr5.3:25020198-25020217 MS.gene58575:intron 45.0%
ACTGATAATCCACCACTGGC+CGG + chr5.3:25019633-25019652 None:intergenic 50.0%
GGCCATGATGACCTCATTGA+TGG - chr5.3:25020219-25020238 MS.gene58575:CDS 50.0%
TATTTCGAGCTATGTGCGCG+AGG - chr5.3:25019654-25019673 MS.gene58575:CDS 50.0%
AATTTACGCTGACCGGCCAG+TGG - chr5.3:25019618-25019637 MS.gene58575:CDS 55.0%
GAGCTATGTGCGCGAGGTGA+AGG - chr5.3:25019660-25019679 MS.gene58575:CDS 60.0%
TTACGCTGACCGGCCAGTGG+TGG - chr5.3:25019621-25019640 MS.gene58575:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 25019610 25020272 25019610 ID=MS.gene58575
chr5.3 mRNA 25019610 25020272 25019610 ID=MS.gene58575.t1;Parent=MS.gene58575
chr5.3 exon 25020201 25020272 25020201 ID=MS.gene58575.t1.exon1;Parent=MS.gene58575.t1
chr5.3 CDS 25020201 25020272 25020201 ID=cds.MS.gene58575.t1;Parent=MS.gene58575.t1
chr5.3 exon 25020001 25020105 25020001 ID=MS.gene58575.t1.exon2;Parent=MS.gene58575.t1
chr5.3 CDS 25020001 25020105 25020001 ID=cds.MS.gene58575.t1;Parent=MS.gene58575.t1
chr5.3 exon 25019610 25019681 25019610 ID=MS.gene58575.t1.exon3;Parent=MS.gene58575.t1
chr5.3 CDS 25019610 25019681 25019610 ID=cds.MS.gene58575.t1;Parent=MS.gene58575.t1
Gene Sequence

>MS.gene58575

ATGAAAAGAATTTACGCTGACCGGCCAGTGGTGGATTATCAGTATATTTCGAGCTATGTGCGCGAGGTGAAGGTAAGTTATATTATGGATTCTTTCACACATATATGTTTTGAGTGTAGAATTATCAATAGTTTTGATGAGCCTAATAGATATTTTTTTTCATGCAGAATCGATTTCAACATGCTGATCAACGTCATATATATTTATCGTTTCTAGAGATGCTGTCAAAGTATATAGAAAGAGAAAAGACTGTTGGTAATGTTATTAGTGAGGTATGTGTTGTTTAATTATGTCATGTGGTCACAATTATAATTGAGGCATAGTGAAATGATATTGGTAAAAACATTTTGAAACAACTTTTAAAATAATATTTTTATTGGAAAAAAAACAATAGTGTGAAATAGGGACAGAGAGAAAGAAAAAAAAAAAAGTAAAAATTGTTTATGTCATGTGGTCAAAATTACAATTGAGATACCATAAAAATACTATTGCTATCATAATTGCACCTCTAAACTACAATTACATATATGCCTTTTTATTTTTCTTTCCTCTTGTGTAATACTCATTTTAATTATGATTTTACTTCTTCAGGTTGCTGAGCTTTTTGAAGGCCATGATGACCTCATTGATGGGTTTACAAATTTCATTCCTCTACGTGGCTAG
Protein sequence

>MS.gene58575.t1

MKRIYADRPVVDYQYISSYVREVKNRFQHADQRHIYLSFLEMLSKYIEREKTVGNVISEVAELFEGHDDLIDGFTNFIPLRG