AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene46971

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46971.t1 MTR_3g449200 93.750 176 11 0 1 176 1 176 1.53e-111 315
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 57 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAATCCTCGCCAATCGTTTC+TGG 0.162291 3.1:-31614339 None:intergenic
ATGAGAGCGCGTGGTGGTTT+CGG 0.298071 3.1:-31614077 None:intergenic
GATCCGACGATCGGAGTTAC+TGG 0.318047 3.1:-31614317 None:intergenic
GCGCGTGGTGGTTTCGGAAT+TGG 0.324550 3.1:-31614071 None:intergenic
GGTGGTTTCGGAATTGGATT+CGG 0.353642 3.1:-31614065 None:intergenic
TCGGAATTGGATTCGGGTAA+CGG 0.371819 3.1:-31614058 None:intergenic
GTGAGAGAGTGGTAGTAAAA+AGG 0.372256 3.1:-31614015 None:intergenic
GTGGTTTCGGAATTGGATTC+GGG 0.381893 3.1:-31614064 None:intergenic
GGATTCACGGTGGTGGGGTC+AGG 0.383442 3.1:+31614356 MS.gene46971:CDS
GGTGTCGTGTTGTTGTGTTT+TGG 0.389261 3.1:-31614107 None:intergenic
CGGAATTGGATTCGGGTAAC+GGG 0.405337 3.1:-31614057 None:intergenic
TTGGCGAGGATTCACGGTGG+TGG 0.422569 3.1:+31614349 MS.gene46971:CDS
AATAGAAGTGACTCTGGTTA+TGG 0.445343 3.1:-31613972 None:intergenic
TGGCGAGGATTCACGGTGGT+GGG 0.445740 3.1:+31614350 MS.gene46971:CDS
AAACGATTGGCGAGGATTCA+CGG 0.464624 3.1:+31614343 MS.gene46971:CDS
ACGGTGGTGGGGTCAGGTAC+CGG 0.470016 3.1:+31614362 MS.gene46971:CDS
GGGTGGATGTGACGGTTGAT+TGG 0.473301 3.1:-31614187 None:intergenic
CGACAACGACGGTGAGATAA+CGG 0.480088 3.1:-31614238 None:intergenic
AAGATCATGTCGTTGCCGTA+AGG 0.485439 3.1:-31614283 None:intergenic
TGGGGTCAGGTACCGGCCGA+TGG 0.490608 3.1:+31614369 MS.gene46971:CDS
AACGGCAATATGCGTTGCTG+TGG 0.521845 3.1:-31614208 None:intergenic
CGATTTCATTCGCCGTGATG+AGG 0.538711 3.1:+31614405 MS.gene46971:CDS
GGCGAGGATTCACGGTGGTG+GGG 0.538778 3.1:+31614351 MS.gene46971:CDS
AAGGAAGAGTAAAACGGTGA+TGG 0.539615 3.1:-31613996 None:intergenic
TCTCACCGTCGTTGTCGTCA+CGG 0.543181 3.1:+31614244 MS.gene46971:CDS
CACCGCCGTCAGATCCCTTA+CGG 0.546747 3.1:+31614268 MS.gene46971:CDS
TCGTTTCTGGATCCGACGAT+CGG 0.553335 3.1:-31614326 None:intergenic
AGTTAACGGAACGTGGTCGA+TGG 0.554931 3.1:-31614149 None:intergenic
ATCGCGGGCGCGTGAGAGAG+TGG 0.558600 3.1:-31614026 None:intergenic
GGATGTGACGGTTGATTGGA+CGG 0.559632 3.1:-31614183 None:intergenic
CGGAAATCGAGGAAAGTTAA+CGG 0.560543 3.1:-31614163 None:intergenic
TTTCATTCGCCGTGATGAGG+AGG 0.563953 3.1:+31614408 MS.gene46971:CDS
GGTTGATTGGACGGAAATCG+AGG 0.564608 3.1:-31614174 None:intergenic
TCGTCGTCATCATGATGAGA+AGG 0.566840 3.1:+31614432 MS.gene46971:CDS
GTCATCATGATGAGAAGGGT+TGG 0.572581 3.1:+31614437 MS.gene46971:CDS
TGAGATAACGGAAAGTCTAA+CGG 0.576695 3.1:-31614226 None:intergenic
GATGGAAATAGAAGTGACTC+TGG 0.580506 3.1:-31613978 None:intergenic
GTTGCTGTGGGTGGATGTGA+CGG 0.586166 3.1:-31614195 None:intergenic
AGTGACTCTGGTTATGGCCA+TGG 0.597966 3.1:-31613966 None:intergenic
AGATCATGTCGTTGCCGTAA+GGG 0.599013 3.1:-31614282 None:intergenic
GCAATATGCGTTGCTGTGGG+TGG 0.602612 3.1:-31614204 None:intergenic
CGTTGCCGTAAGGGATCTGA+CGG 0.605253 3.1:-31614273 None:intergenic
ATGCCAGTAACTCCGATCGT+CGG 0.606961 3.1:+31614314 MS.gene46971:CDS
CGAGGAAAGTTAACGGAACG+TGG 0.607466 3.1:-31614156 None:intergenic
GGAGTTGAGATTGAACGAAA+CGG 0.615506 3.1:-31614128 None:intergenic
CGTCGTCATCATGATGAGAA+GGG 0.619870 3.1:+31614433 MS.gene46971:CDS
TCGTCGGATCCAGAAACGAT+TGG 0.624574 3.1:+31614330 MS.gene46971:CDS
GGGAGAACTATGAGAGCGCG+TGG 0.627969 3.1:-31614086 None:intergenic
TCGTTATAAGTCATCACCAT+CGG 0.635222 3.1:-31614385 None:intergenic
TATAAGTCATCACCATCGGC+CGG 0.644387 3.1:-31614381 None:intergenic
TGCCGTAAGGGATCTGACGG+CGG 0.663675 3.1:-31614270 None:intergenic
ACGGCAATATGCGTTGCTGT+GGG 0.667789 3.1:-31614207 None:intergenic
GGATCCAGAAACGATTGGCG+AGG 0.676844 3.1:+31614335 MS.gene46971:CDS
GACGACGATCCTCCTCATCA+CGG 0.685950 3.1:-31614417 None:intergenic
GGTGACCGTGACGACAACGA+CGG 0.709494 3.1:-31614249 None:intergenic
AGAACTATGAGAGCGCGTGG+TGG 0.721678 3.1:-31614083 None:intergenic
CGATTGGCGAGGATTCACGG+TGG 0.837336 3.1:+31614346 MS.gene46971:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGTAAAAAGGAAGAGTAAAA+CGG - chr3.1:31614005-31614024 None:intergenic 25.0%
AATAGAAGTGACTCTGGTTA+TGG - chr3.1:31613975-31613994 None:intergenic 35.0%
TCGTTATAAGTCATCACCAT+CGG - chr3.1:31614388-31614407 None:intergenic 35.0%
!! TGAGATAACGGAAAGTCTAA+CGG - chr3.1:31614229-31614248 None:intergenic 35.0%
AAGGAAGAGTAAAACGGTGA+TGG - chr3.1:31613999-31614018 None:intergenic 40.0%
CGGAAATCGAGGAAAGTTAA+CGG - chr3.1:31614166-31614185 None:intergenic 40.0%
GATGGAAATAGAAGTGACTC+TGG - chr3.1:31613981-31614000 None:intergenic 40.0%
GGAGTTGAGATTGAACGAAA+CGG - chr3.1:31614131-31614150 None:intergenic 40.0%
GTGAGAGAGTGGTAGTAAAA+AGG - chr3.1:31614018-31614037 None:intergenic 40.0%
!! GTGTCGTGTTGTTGTGTTTT+GGG - chr3.1:31614109-31614128 None:intergenic 40.0%
AAACGATTGGCGAGGATTCA+CGG + chr3.1:31614343-31614362 MS.gene46971:CDS 45.0%
AAGATCATGTCGTTGCCGTA+AGG - chr3.1:31614286-31614305 None:intergenic 45.0%
AGATCATGTCGTTGCCGTAA+GGG - chr3.1:31614285-31614304 None:intergenic 45.0%
CGTCGTCATCATGATGAGAA+GGG + chr3.1:31614433-31614452 MS.gene46971:CDS 45.0%
GGTGGTTTCGGAATTGGATT+CGG - chr3.1:31614068-31614087 None:intergenic 45.0%
GTCATCATGATGAGAAGGGT+TGG + chr3.1:31614437-31614456 MS.gene46971:CDS 45.0%
GTGGTTTCGGAATTGGATTC+GGG - chr3.1:31614067-31614086 None:intergenic 45.0%
TATAAGTCATCACCATCGGC+CGG - chr3.1:31614384-31614403 None:intergenic 45.0%
TCGGAATTGGATTCGGGTAA+CGG - chr3.1:31614061-31614080 None:intergenic 45.0%
TCGTCGTCATCATGATGAGA+AGG + chr3.1:31614432-31614451 MS.gene46971:CDS 45.0%
!! GGTGTCGTGTTGTTGTGTTT+TGG - chr3.1:31614110-31614129 None:intergenic 45.0%
!!! GTAACGGGTTTTGAAGATCG+CGG - chr3.1:31614045-31614064 None:intergenic 45.0%
!!! TAACGGGTTTTGAAGATCGC+GGG - chr3.1:31614044-31614063 None:intergenic 45.0%
AACGGCAATATGCGTTGCTG+TGG - chr3.1:31614211-31614230 None:intergenic 50.0%
ACGGCAATATGCGTTGCTGT+GGG - chr3.1:31614210-31614229 None:intergenic 50.0%
AGTTAACGGAACGTGGTCGA+TGG - chr3.1:31614152-31614171 None:intergenic 50.0%
ATGCCAGTAACTCCGATCGT+CGG + chr3.1:31614314-31614333 MS.gene46971:CDS 50.0%
CGACAACGACGGTGAGATAA+CGG - chr3.1:31614241-31614260 None:intergenic 50.0%
CGAGGAAAGTTAACGGAACG+TGG - chr3.1:31614159-31614178 None:intergenic 50.0%
CGATTTCATTCGCCGTGATG+AGG + chr3.1:31614405-31614424 MS.gene46971:CDS 50.0%
CGGAATTGGATTCGGGTAAC+GGG - chr3.1:31614060-31614079 None:intergenic 50.0%
GAATCCTCGCCAATCGTTTC+TGG - chr3.1:31614342-31614361 None:intergenic 50.0%
GGATGTGACGGTTGATTGGA+CGG - chr3.1:31614186-31614205 None:intergenic 50.0%
GGTTGATTGGACGGAAATCG+AGG - chr3.1:31614177-31614196 None:intergenic 50.0%
TCGTCGGATCCAGAAACGAT+TGG + chr3.1:31614330-31614349 MS.gene46971:CDS 50.0%
TTTCATTCGCCGTGATGAGG+AGG + chr3.1:31614408-31614427 MS.gene46971:CDS 50.0%
! TCGTTTCTGGATCCGACGAT+CGG - chr3.1:31614329-31614348 None:intergenic 50.0%
CGTTGCCGTAAGGGATCTGA+CGG - chr3.1:31614276-31614295 None:intergenic 55.0%
GACGACGATCCTCCTCATCA+CGG - chr3.1:31614420-31614439 None:intergenic 55.0%
GATCCGACGATCGGAGTTAC+TGG - chr3.1:31614320-31614339 None:intergenic 55.0%
GCAATATGCGTTGCTGTGGG+TGG - chr3.1:31614207-31614226 None:intergenic 55.0%
GGATCCAGAAACGATTGGCG+AGG + chr3.1:31614335-31614354 MS.gene46971:CDS 55.0%
GGGTGGATGTGACGGTTGAT+TGG - chr3.1:31614190-31614209 None:intergenic 55.0%
GTTGCTGTGGGTGGATGTGA+CGG - chr3.1:31614198-31614217 None:intergenic 55.0%
TCTCACCGTCGTTGTCGTCA+CGG + chr3.1:31614244-31614263 MS.gene46971:CDS 55.0%
! AGAACTATGAGAGCGCGTGG+TGG - chr3.1:31614086-31614105 None:intergenic 55.0%
! ATGAGAGCGCGTGGTGGTTT+CGG - chr3.1:31614080-31614099 None:intergenic 55.0%
CACCGCCGTCAGATCCCTTA+CGG + chr3.1:31614268-31614287 MS.gene46971:CDS 60.0%
CGATTGGCGAGGATTCACGG+TGG + chr3.1:31614346-31614365 MS.gene46971:CDS 60.0%
GCGCGTGGTGGTTTCGGAAT+TGG - chr3.1:31614074-31614093 None:intergenic 60.0%
GGTGACCGTGACGACAACGA+CGG - chr3.1:31614252-31614271 None:intergenic 60.0%
TGCCGTAAGGGATCTGACGG+CGG - chr3.1:31614273-31614292 None:intergenic 60.0%
TGGCGAGGATTCACGGTGGT+GGG + chr3.1:31614350-31614369 MS.gene46971:CDS 60.0%
TTGGCGAGGATTCACGGTGG+TGG + chr3.1:31614349-31614368 MS.gene46971:CDS 60.0%
! GGGAGAACTATGAGAGCGCG+TGG - chr3.1:31614089-31614108 None:intergenic 60.0%
GGCGAGGATTCACGGTGGTG+GGG + chr3.1:31614351-31614370 MS.gene46971:CDS 65.0%
!! ACGGTGGTGGGGTCAGGTAC+CGG + chr3.1:31614362-31614381 MS.gene46971:CDS 65.0%
!! GGATTCACGGTGGTGGGGTC+AGG + chr3.1:31614356-31614375 MS.gene46971:CDS 65.0%
ATCGCGGGCGCGTGAGAGAG+TGG - chr3.1:31614029-31614048 None:intergenic 70.0%
!! TGGGGTCAGGTACCGGCCGA+TGG + chr3.1:31614369-31614388 MS.gene46971:CDS 70.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 31613968 31614498 31613968 ID=MS.gene46971
chr3.1 mRNA 31613968 31614498 31613968 ID=MS.gene46971.t1;Parent=MS.gene46971
chr3.1 exon 31613968 31614498 31613968 ID=MS.gene46971.t1.exon1;Parent=MS.gene46971.t1
chr3.1 CDS 31613968 31614498 31613968 ID=cds.MS.gene46971.t1;Parent=MS.gene46971.t1
Gene Sequence

>MS.gene46971

ATGGCCATAACCAGAGTCACTTCTATTTCCATCACCGTTTTACTCTTCCTTTTTACTACCACTCTCTCACGCGCCCGCGATCTTCAAAACCCGTTACCCGAATCCAATTCCGAAACCACCACGCGCTCTCATAGTTCTCCCAAAACACAACAACACGACACCGTTTCGTTCAATCTCAACTCCATCGACCACGTTCCGTTAACTTTCCTCGATTTCCGTCCAATCAACCGTCACATCCACCCACAGCAACGCATATTGCCGTTAGACTTTCCGTTATCTCACCGTCGTTGTCGTCACGGTCACCGCCGTCAGATCCCTTACGGCAACGACATGATCTTGTCGAAAGATGCCAGTAACTCCGATCGTCGGATCCAGAAACGATTGGCGAGGATTCACGGTGGTGGGGTCAGGTACCGGCCGATGGTGATGACTTATAACGATTTCATTCGCCGTGATGAGGAGGATCGTCGTCATCATGATGAGAAGGGTTGGTTTGAGAAGAAGATTCATGAGTTGTTGAACTTGTTCTAA
Protein sequence

>MS.gene46971.t1

MAITRVTSISITVLLFLFTTTLSRARDLQNPLPESNSETTTRSHSSPKTQQHDTVSFNLNSIDHVPLTFLDFRPINRHIHPQQRILPLDFPLSHRRCRHGHRRQIPYGNDMILSKDASNSDRRIQKRLARIHGGGVRYRPMVMTYNDFIRRDEEDRRHHDEKGWFEKKIHELLNLF