AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054954


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054954.t1 MTR_3g096290 89.634 164 12 1 1 164 1 159 4.39e-100 285
MS.gene054954.t1 MTR_3g096290 86.066 122 12 1 1 122 9 125 1.96e-65 197
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054954.t1 AT1G74880 72.500 120 33 0 45 164 39 158 7.55e-63 191

Find 44 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTCTTAGGAAGAGTCTT+AGG 0.205905 3.1:+76644340 None:intergenic
GTAGTCTAATCCTTTGTAAT+AGG 0.224129 3.1:+76644036 None:intergenic
CTGGAATAAACAGGTTTCTT+AGG 0.242562 3.1:+76644328 None:intergenic
CTTGACTCACTGGAATAAAC+AGG 0.396415 3.1:+76644319 None:intergenic
GATATGCGTATATTTGAAAC+AGG 0.408664 3.1:-76643896 MS.gene054954:CDS
TCTTGAACTGCACGAATCAA+TGG 0.413571 3.1:+76644451 None:intergenic
GTTTCTTAGGAAGAGTCTTA+GGG 0.440236 3.1:+76644341 None:intergenic
TGCTTAATTCTCAGGTTGCA+TGG 0.442545 3.1:-76643683 MS.gene054954:intron
GCAGTTCAAGACGGTGAACC+AGG 0.447486 3.1:-76644439 MS.gene054954:CDS
TAGTCTAATCCTTTGTAATA+GGG 0.459657 3.1:+76644037 None:intergenic
GCATCAGAGCTCTTAGTTTG+TGG 0.477417 3.1:+76644403 None:intergenic
TTTGAGAAATGGGAAAGAGA+AGG 0.496635 3.1:+76644508 None:intergenic
CTTGAACTGCACGAATCAAT+GGG 0.503362 3.1:+76644452 None:intergenic
GGAAGCCAAGCTGGAGCAGT+GGG 0.508111 3.1:+76643651 None:intergenic
AGGAAGAGTCTTAGGGGCAG+TGG 0.518025 3.1:+76644348 None:intergenic
ATGGGAAAGAGAAGGAAAGG+AGG 0.524817 3.1:+76644516 None:intergenic
CTGAGCACTACTAGAGGCTG+AGG 0.528832 3.1:+76644378 None:intergenic
GAAATGGGAAAGAGAAGGAA+AGG 0.530112 3.1:+76644513 None:intergenic
GCTTAATTCTCAGGTTGCAT+GGG 0.543172 3.1:-76643682 MS.gene054954:intron
TCCTACATACATGCTTATCA+AGG 0.544432 3.1:-76643631 MS.gene054954:intron
AGGAAGCCAAGCTGGAGCAG+TGG 0.544685 3.1:+76643650 None:intergenic
GAGTCCCCACTGCTCCAGCT+TGG 0.545534 3.1:-76643656 MS.gene054954:CDS
AATTTGTGGACAGTGAAGAA+AGG 0.549691 3.1:-76644219 MS.gene054954:intron
AATTCTCAGGTTGCATGGGT+AGG 0.550094 3.1:-76643678 MS.gene054954:intron
TCTAATCCTTTGTAATAGGG+TGG 0.556199 3.1:+76644040 None:intergenic
TGAAGAAAGGTCAGATTGTG+AGG 0.558487 3.1:-76644206 MS.gene054954:CDS
ATGTATGTAGGAAGCCAAGC+TGG 0.563654 3.1:+76643642 None:intergenic
GGGCACCCACCCTATTACAA+AGG 0.572065 3.1:-76644046 MS.gene054954:CDS
TCAGATTGTGAGGGTGGACA+AGG 0.576125 3.1:-76644196 MS.gene054954:CDS
GAAAGGTCAGATTGTGAGGG+TGG 0.585375 3.1:-76644202 MS.gene054954:CDS
CTAATCCTTTGTAATAGGGT+GGG 0.595783 3.1:+76644041 None:intergenic
CAGTTCAAGACGGTGAACCA+GGG 0.597426 3.1:-76644438 MS.gene054954:CDS
TTGATTCGTGCAGTTCAAGA+CGG 0.616062 3.1:-76644448 MS.gene054954:CDS
TTTGTTTGTTTACCTCACCA+CGG 0.617430 3.1:+76644002 None:intergenic
AGTTCAAGACGGTGAACCAG+GGG 0.628235 3.1:-76644437 MS.gene054954:CDS
ACCTTGATAAGCATGTATGT+AGG 0.632174 3.1:+76643630 None:intergenic
GAATCAATGGGAAAGAAGAA+CGG 0.633893 3.1:+76644464 None:intergenic
TTTCTTAGGAAGAGTCTTAG+GGG 0.641863 3.1:+76644342 None:intergenic
GAAGAAAGGTCAGATTGTGA+GGG 0.659835 3.1:-76644205 MS.gene054954:CDS
GACTACATTTACGAAGACCG+TGG 0.695548 3.1:-76644019 MS.gene054954:CDS
TGAAGACTGAGCACTACTAG+AGG 0.702291 3.1:+76644372 None:intergenic
CATTTACGAAGACCGTGGTG+AGG 0.713150 3.1:-76644014 MS.gene054954:intron
GTTCAAGACGGTGAACCAGG+GGG 0.724086 3.1:-76644436 MS.gene054954:CDS
GAAGCCAAGCTGGAGCAGTG+GGG 0.758823 3.1:+76643652 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTTGTGTAAAAAAATTAT+TGG + chr3.1:76644208-76644227 None:intergenic 15.0%
!!! ATTTTGTTTTCATAATCTTT+TGG + chr3.1:76644030-76644049 None:intergenic 15.0%
!!! TATTCATTTTTGTTAATTTG+TGG - chr3.1:76643771-76643790 MS.gene054954:intron 15.0%
! AAATGTCAAACTGTATTTGT+AGG - chr3.1:76644080-76644099 MS.gene054954:intron 25.0%
! AGATACTGAAAAATTAACCT+TGG + chr3.1:76643931-76643950 None:intergenic 25.0%
! ATTTCTCAAAAACTTTGACA+AGG - chr3.1:76643509-76643528 MS.gene054954:intron 25.0%
! TAGTCTAATCCTTTGTAATA+GGG + chr3.1:76643970-76643989 None:intergenic 25.0%
!! GTTTTCTATGATTCCAATTA+TGG - chr3.1:76644240-76644259 MS.gene054954:intron 25.0%
!!! ATTTTTCAGTATCTTTCTGT+TGG - chr3.1:76643937-76643956 MS.gene054954:intron 25.0%
!!! TGTCAAAGTTTTTGAGAAAT+GGG + chr3.1:76643509-76643528 None:intergenic 25.0%
!!! TTGTCAAAGTTTTTGAGAAA+TGG + chr3.1:76643510-76643529 None:intergenic 25.0%
!!! TTTTTCAGTATCTTTCTGTT+GGG - chr3.1:76643938-76643957 MS.gene054954:intron 25.0%
CAACAAAAAAAGTAAGAGTG+AGG + chr3.1:76644517-76644536 None:intergenic 30.0%
CTTCACAATGTTACCATAAT+TGG + chr3.1:76644256-76644275 None:intergenic 30.0%
GTAGTCTAATCCTTTGTAAT+AGG + chr3.1:76643971-76643990 None:intergenic 30.0%
TAATGCTTTACTTGTTCCAA+TGG - chr3.1:76644396-76644415 MS.gene054954:CDS 30.0%
! GATATGCGTATATTTGAAAC+AGG - chr3.1:76644108-76644127 MS.gene054954:intron 30.0%
AATTTGTGGACAGTGAAGAA+AGG - chr3.1:76643785-76643804 MS.gene054954:intron 35.0%
ACCTTGATAAGCATGTATGT+AGG + chr3.1:76644377-76644396 None:intergenic 35.0%
CAAACTGTATTTGTAGGTCT+TGG - chr3.1:76644086-76644105 MS.gene054954:intron 35.0%
CTAATCCTTTGTAATAGGGT+GGG + chr3.1:76643966-76643985 None:intergenic 35.0%
CTGGAATAAACAGGTTTCTT+AGG + chr3.1:76643679-76643698 None:intergenic 35.0%
GAATCAATGGGAAAGAAGAA+CGG + chr3.1:76643543-76643562 None:intergenic 35.0%
GTTTCTTAGGAAGAGTCTTA+GGG + chr3.1:76643666-76643685 None:intergenic 35.0%
TATTAGATTGTAGCAGCCAT+TGG + chr3.1:76644415-76644434 None:intergenic 35.0%
TCCTACATACATGCTTATCA+AGG - chr3.1:76644373-76644392 MS.gene054954:CDS 35.0%
TCTAATCCTTTGTAATAGGG+TGG + chr3.1:76643967-76643986 None:intergenic 35.0%
TGTACCATTGCTTAATTCTC+AGG - chr3.1:76644313-76644332 MS.gene054954:intron 35.0%
TTTCTTAGGAAGAGTCTTAG+GGG + chr3.1:76643665-76643684 None:intergenic 35.0%
TTTGAGAAATGGGAAAGAGA+AGG + chr3.1:76643499-76643518 None:intergenic 35.0%
TTTGTTTGTTTACCTCACCA+CGG + chr3.1:76644005-76644024 None:intergenic 35.0%
CTTGAACTGCACGAATCAAT+GGG + chr3.1:76643555-76643574 None:intergenic 40.0%
CTTGACTCACTGGAATAAAC+AGG + chr3.1:76643688-76643707 None:intergenic 40.0%
GAAATGGGAAAGAGAAGGAA+AGG + chr3.1:76643494-76643513 None:intergenic 40.0%
GAAGAAAGGTCAGATTGTGA+GGG - chr3.1:76643799-76643818 MS.gene054954:intron 40.0%
GCAACCTGAGAATTAAGCAA+TGG + chr3.1:76644320-76644339 None:intergenic 40.0%
GGACTCAAATAACATGTCCA+AGG - chr3.1:76643911-76643930 MS.gene054954:intron 40.0%
GGTTTCTTAGGAAGAGTCTT+AGG + chr3.1:76643667-76643686 None:intergenic 40.0%
TAGTTATGTCAGCTGTGAGT+AGG - chr3.1:76643887-76643906 MS.gene054954:CDS 40.0%
TATTTGGTTGCTTGACTCAC+TGG + chr3.1:76643698-76643717 None:intergenic 40.0%
TCTTGAACTGCACGAATCAA+TGG + chr3.1:76643556-76643575 None:intergenic 40.0%
TGAAGAAAGGTCAGATTGTG+AGG - chr3.1:76643798-76643817 MS.gene054954:intron 40.0%
! GCTTAATTCTCAGGTTGCAT+GGG - chr3.1:76644322-76644341 MS.gene054954:intron 40.0%
! TGCTTAATTCTCAGGTTGCA+TGG - chr3.1:76644321-76644340 MS.gene054954:intron 40.0%
! TTGATTCGTGCAGTTCAAGA+CGG - chr3.1:76643556-76643575 MS.gene054954:intron 40.0%
ATGGGAAAGAGAAGGAAAGG+AGG + chr3.1:76643491-76643510 None:intergenic 45.0%
ATGTATGTAGGAAGCCAAGC+TGG + chr3.1:76644365-76644384 None:intergenic 45.0%
GACTACATTTACGAAGACCG+TGG - chr3.1:76643985-76644004 MS.gene054954:intron 45.0%
TGAAGACTGAGCACTACTAG+AGG + chr3.1:76643635-76643654 None:intergenic 45.0%
TTATGTCAGCTGTGAGTAGG+AGG - chr3.1:76643890-76643909 MS.gene054954:CDS 45.0%
! AATTCTCAGGTTGCATGGGT+AGG - chr3.1:76644326-76644345 MS.gene054954:intron 45.0%
! GCATCAGAGCTCTTAGTTTG+TGG + chr3.1:76643604-76643623 None:intergenic 45.0%
!! AATTCAAATAAATATTTATT+TGG + chr3.1:76643714-76643733 None:intergenic 5.0%
AGTTCAAGACGGTGAACCAG+GGG - chr3.1:76643567-76643586 MS.gene054954:intron 50.0%
CAGTTCAAGACGGTGAACCA+GGG - chr3.1:76643566-76643585 MS.gene054954:intron 50.0%
CATTTACGAAGACCGTGGTG+AGG - chr3.1:76643990-76644009 MS.gene054954:intron 50.0%
GAAAGGTCAGATTGTGAGGG+TGG - chr3.1:76643802-76643821 MS.gene054954:intron 50.0%
GTCAGTAGTGTGTGTGCTGT+AGG - chr3.1:76644155-76644174 MS.gene054954:intron 50.0%
GTGCTGTAGGTGTGAACCAA+AGG - chr3.1:76644168-76644187 MS.gene054954:intron 50.0%
TCAGATTGTGAGGGTGGACA+AGG - chr3.1:76643808-76643827 MS.gene054954:intron 50.0%
AGGAAGAGTCTTAGGGGCAG+TGG + chr3.1:76643659-76643678 None:intergenic 55.0%
CTGAGCACTACTAGAGGCTG+AGG + chr3.1:76643629-76643648 None:intergenic 55.0%
GCAGTTCAAGACGGTGAACC+AGG - chr3.1:76643565-76643584 MS.gene054954:intron 55.0%
GGGCACCCACCCTATTACAA+AGG - chr3.1:76643958-76643977 MS.gene054954:intron 55.0%
GTTCAAGACGGTGAACCAGG+GGG - chr3.1:76643568-76643587 MS.gene054954:intron 55.0%
AGGAAGCCAAGCTGGAGCAG+TGG + chr3.1:76644357-76644376 None:intergenic 60.0%
GAAGCCAAGCTGGAGCAGTG+GGG + chr3.1:76644355-76644374 None:intergenic 60.0%
GGAAGCCAAGCTGGAGCAGT+GGG + chr3.1:76644356-76644375 None:intergenic 60.0%
GGCATGCTGTCAGCTGCCTT+TGG + chr3.1:76644187-76644206 None:intergenic 60.0%
GAGTCCCCACTGCTCCAGCT+TGG - chr3.1:76644348-76644367 MS.gene054954:CDS 65.0%
TGTGGCTGTGTACTGCCCCC+TGG + chr3.1:76643586-76643605 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 76643457 76644569 76643457 ID=MS.gene054954
chr3.1 mRNA 76643457 76644569 76643457 ID=MS.gene054954.t1;Parent=MS.gene054954
chr3.1 exon 76644329 76644569 76644329 ID=MS.gene054954.t1.exon1;Parent=MS.gene054954.t1
chr3.1 CDS 76644329 76644569 76644329 ID=cds.MS.gene054954.t1;Parent=MS.gene054954.t1
chr3.1 exon 76644173 76644228 76644173 ID=MS.gene054954.t1.exon2;Parent=MS.gene054954.t1
chr3.1 CDS 76644173 76644228 76644173 ID=cds.MS.gene054954.t1;Parent=MS.gene054954.t1
chr3.1 exon 76644015 76644080 76644015 ID=MS.gene054954.t1.exon3;Parent=MS.gene054954.t1
chr3.1 CDS 76644015 76644080 76644015 ID=cds.MS.gene054954.t1;Parent=MS.gene054954.t1
chr3.1 exon 76643883 76643924 76643883 ID=MS.gene054954.t1.exon4;Parent=MS.gene054954.t1
chr3.1 CDS 76643883 76643924 76643883 ID=cds.MS.gene054954.t1;Parent=MS.gene054954.t1
chr3.1 exon 76643632 76643691 76643632 ID=MS.gene054954.t1.exon5;Parent=MS.gene054954.t1
chr3.1 CDS 76643632 76643691 76643632 ID=cds.MS.gene054954.t1;Parent=MS.gene054954.t1
chr3.1 exon 76643457 76643486 76643457 ID=MS.gene054954.t1.exon6;Parent=MS.gene054954.t1
chr3.1 CDS 76643457 76643486 76643457 ID=cds.MS.gene054954.t1;Parent=MS.gene054954.t1
Gene Sequence

>MS.gene054954

ATGGCTTTCTGTGTAACTCTCTGCTACTACACCTCCTTTCCTTCTCTTTCCCATTTCTCAAAAACTTTGACAAGGAAACATGTCCGTTCTTCTTTCCCATTGATTCGTGCAGTTCAAGACGGTGAACCAGGGGGCAGTACACAGCCACAAACTAAGAGCTCTGATGCTTCCTCAGCCTCTAGTAGTGCTCAGTCTTCAACCACTGCCCCTAAGACTCTTCCTAAGAAACCTGTTTATTCCAGTGAGTCAAGCAACCAAATAAATATTTATTTGAATTTTATATATATACTGAATGCTGCTGCTGTCTGTGTGAGTATTCATTTTTGTTAATTTGTGGACAGTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCATCAATGTAAGAAGACTATTATTGATTTAGTTTCAATTATAGTTATGTCAGCTGTGAGTAGGAGGACTCAAATAACATGTCCAAGGTTAATTTTTCAGTATCTTTCTGTTGGGCACCCACCCTATTACAAAGGATTAGACTACATTTACGAAGACCGTGGTGAGGTAAACAAACAAACACCAAAAGATTATGAAAACAAAATACTTTATATGATTAGTGTTTATCTAACTAGAAATGTCAAACTGTATTTGTAGGTCTTGGATATGCGTATATTTGAAACAGGAGAGCATGCACTTGTAAGTAACTTGTCAGTAGTGTGTGTGCTGTAGGTGTGAACCAAAGGCAGCTGACAGCATGCCAATAATTTTTTTACACAAACAACATGACTATTTGTTTTCTATGATTCCAATTATGGTAACATTGTGAAGTATGTGAAGTTTAAGTTTTATTATTGTGACACAAAACTGTACCATTGCTTAATTCTCAGGTTGCATGGGTAGGAGTCCCCACTGCTCCAGCTTGGCTTCCTACATACATGCTTATCAAGGTAATGCTTTACTTGTTCCAATGGCTGCTACAATCTAATAGTAAATGAAATCTGATGTAAATTGTTTATTTTTATCTACATTTACATGACTTCTTTACATTTTAGTTGCTTTGAAAGCACCTCACTCTTACTTTTTTTGTTGCAGTCAGAGAAGCTCAATTATGAGAGACTATAA

Protein sequence

>MS.gene054954.t1

MAFCVTLCYYTSFPSLSHFSKTLTRKHVRSSFPLIRAVQDGEPGGSTQPQTKSSDASSASSSAQSSTTAPKTLPKKPVYSMKKGQIVRVDKEKYLNSINYLSVGHPPYYKGLDYIYEDRGEVLDMRIFETGEHALVAWVGVPTAPAWLPTYMLIKSEKLNYERL