AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene018969

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene018969.t1 MTR_3g438070 100.000 92 0 0 1 92 1 92 3.41e-60 178
MS.gene018969.t1 MTR_7g010120 72.340 94 23 2 1 92 1 93 9.01e-38 122
MS.gene018969.t1 MTR_5g039180 72.727 77 19 1 17 91 17 93 2.66e-33 110
MS.gene018969.t1 MTR_6g011670 73.077 78 19 1 17 92 15 92 1.58e-32 108
MS.gene018969.t1 MTR_7g059260 48.611 72 37 0 8 79 3 74 2.92e-11 54.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene018969.t1 AT3G47710 73.118 93 23 2 1 92 1 92 2.65e-39 125
MS.gene018969.t1 AT1G74500 77.922 77 16 1 17 92 17 93 9.44e-36 117
MS.gene018969.t1 AT1G26945 79.730 74 13 1 19 90 19 92 1.49e-34 114
MS.gene018969.t1 AT3G28857 65.957 94 27 3 1 91 1 92 1.45e-32 108
MS.gene018969.t1 AT5G39860 69.231 78 21 2 17 91 15 92 9.71e-30 102
MS.gene018969.t1 AT5G15160 66.667 75 22 2 19 90 18 92 2.48e-27 95.9

Find 15 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGCTTCGAGGGTGTTGC+AGG 0.348972 3.3:-29381523 MS.gene018969:CDS
TGAGCGTTTGTCTGAGCTAT+TGG 0.392203 3.3:-29381451 MS.gene018969:CDS
GAGCTCCTATTGCGAATCTC+TGG 0.433126 3.3:+29382474 None:intergenic
TGGAAGAAGTTGCTGCAACT+TGG 0.461097 3.3:+29382494 None:intergenic
TATATCAGGTTTCAGCTTCG+AGG 0.481740 3.3:-29381533 MS.gene018969:intron
TTCTTCCAGAGATTCGCAAT+AGG 0.499436 3.3:-29382479 MS.gene018969:CDS
ATATCAGGTTTCAGCTTCGA+GGG 0.550730 3.3:-29381532 MS.gene018969:intron
GCTCAGACAAACGCTCACTT+AGG 0.559789 3.3:+29381457 None:intergenic
GCAACTTGGAGACAAGATCA+TGG 0.561243 3.3:+29382508 None:intergenic
AGATGTCTAGCAGGAGGTCA+CGG 0.593324 3.3:-29382575 MS.gene018969:CDS
TCGCAATAGGAGCTCTGACA+AGG 0.593557 3.3:-29382466 MS.gene018969:intron
CTAGCAGGAGGTCACGGTCA+CGG 0.620916 3.3:-29382569 MS.gene018969:CDS
TTATAAAGATGTCTAGCAGG+AGG 0.639084 3.3:-29382581 None:intergenic
AAGATCATGGATCTGATCGT+CGG 0.643584 3.3:+29382521 None:intergenic
CACGGCAAACGAGTAGCTCG+AGG 0.663514 3.3:-29382551 MS.gene018969:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAAAAAACTTGAA+AGG - chr3.3:29382146-29382165 MS.gene018969:intron 10.0%
!! TGTATTAAAAATATAGTATA+TGG + chr3.3:29381752-29381771 None:intergenic 10.0%
!!! ATGACTTTTATAAAAAATAA+TGG + chr3.3:29381658-29381677 None:intergenic 10.0%
!!! TTATTTTTTATAAAAGTCAT+TGG - chr3.3:29381658-29381677 MS.gene018969:intron 10.0%
!!! AAATTGAATTTTACTATATC+AGG - chr3.3:29382424-29382443 MS.gene018969:intron 15.0%
!! AAAAAAAGGAACAACAATAT+AGG - chr3.3:29382274-29382293 MS.gene018969:intron 20.0%
!!! ATATTGTTGTTCCTTTTTTT+TGG + chr3.3:29382274-29382293 None:intergenic 20.0%
! CTAGGAAACAAATAATATGT+AGG + chr3.3:29381537-29381556 None:intergenic 25.0%
! GATAATGCATAATATATGCA+GGG - chr3.3:29381979-29381998 MS.gene018969:intron 25.0%
! TTAAACCAACTTAATCCTAT+AGG - chr3.3:29382236-29382255 MS.gene018969:intron 25.0%
!!! AGAAGAGATTAGTTTTATAG+CGG - chr3.3:29381773-29381792 MS.gene018969:intron 25.0%
ACACTAGAGTAAGTATAAGA+GGG - chr3.3:29382210-29382229 MS.gene018969:intron 30.0%
ACATCAACAATTCTTGTAGA+TGG + chr3.3:29382350-29382369 None:intergenic 30.0%
ACCATACTTATTCACCTTTA+AGG - chr3.3:29382023-29382042 MS.gene018969:intron 30.0%
ACCTTAAAGGTGAATAAGTA+TGG + chr3.3:29382027-29382046 None:intergenic 30.0%
CATCAACAATTCTTGTAGAT+GGG + chr3.3:29382349-29382368 None:intergenic 30.0%
GGATAATGCATAATATATGC+AGG - chr3.3:29381978-29381997 MS.gene018969:intron 30.0%
TACACTAGAGTAAGTATAAG+AGG - chr3.3:29382209-29382228 MS.gene018969:intron 30.0%
! TTTTCTTGGTCAATTATCCT+AGG + chr3.3:29382126-29382145 None:intergenic 30.0%
!! CTAGTCTTTTGATTATGACT+AGG + chr3.3:29381555-29381574 None:intergenic 30.0%
AACTTAATCCTATAGGTCCA+GGG - chr3.3:29382243-29382262 MS.gene018969:intron 35.0%
AGCTCAGAAGGATTTCTTTA+CGG + chr3.3:29381942-29381961 None:intergenic 35.0%
ATATAGGCCTAACAAATACG+AGG - chr3.3:29382290-29382309 MS.gene018969:intron 35.0%
GAGATACCCTATTAATCTAC+CGG - chr3.3:29381817-29381836 MS.gene018969:intron 35.0%
GAGCTTAGTTCATTTGGTAA+GGG - chr3.3:29381957-29381976 MS.gene018969:intron 35.0%
TATAGGCCTAACAAATACGA+GGG - chr3.3:29382291-29382310 MS.gene018969:intron 35.0%
TCTTGTAGATGGGAAAAAAC+TGG + chr3.3:29382339-29382358 None:intergenic 35.0%
TGAGCTTAGTTCATTTGGTA+AGG - chr3.3:29381956-29381975 MS.gene018969:intron 35.0%
TTAATCCCCTCGTATTTGTT+AGG + chr3.3:29382300-29382319 None:intergenic 35.0%
!! TTATTCACCTTTAAGGTCTC+TGG - chr3.3:29382030-29382049 MS.gene018969:intron 35.0%
AAGATCATGGATCTGATCGT+CGG + chr3.3:29381453-29381472 None:intergenic 40.0%
AGGTGAATAAGTATGGTGTC+TGG + chr3.3:29382020-29382039 None:intergenic 40.0%
ATAGGCCTAACAAATACGAG+GGG - chr3.3:29382292-29382311 MS.gene018969:intron 40.0%
ATATCAGGTTTCAGCTTCGA+GGG - chr3.3:29382439-29382458 MS.gene018969:intron 40.0%
CAACTTAATCCTATAGGTCC+AGG - chr3.3:29382242-29382261 MS.gene018969:intron 40.0%
CCAAATGAACTAAGCTCAGA+AGG + chr3.3:29381954-29381973 None:intergenic 40.0%
CCAGGGACATACCAAAAAAA+AGG - chr3.3:29382260-29382279 MS.gene018969:intron 40.0%
CCTTCTGAGCTTAGTTCATT+TGG - chr3.3:29381951-29381970 MS.gene018969:intron 40.0%
CTGGACCTATAGGATTAAGT+TGG + chr3.3:29382244-29382263 None:intergenic 40.0%
GACTCTCCGGTAGATTAATA+GGG + chr3.3:29381826-29381845 None:intergenic 40.0%
GGTGAATAAGTATGGTGTCT+GGG + chr3.3:29382019-29382038 None:intergenic 40.0%
GTGAATAAGTATGGTGTCTG+GGG + chr3.3:29382018-29382037 None:intergenic 40.0%
TATATCAGGTTTCAGCTTCG+AGG - chr3.3:29382438-29382457 MS.gene018969:intron 40.0%
TGACTCTCCGGTAGATTAAT+AGG + chr3.3:29381827-29381846 None:intergenic 40.0%
TGCATAATATATGCAGGGAC+CGG - chr3.3:29381984-29382003 MS.gene018969:intron 40.0%
TTCTTCCAGAGATTCGCAAT+AGG - chr3.3:29381492-29381511 MS.gene018969:CDS 40.0%
!! GAGCTGTTTTGTGAGCTTTT+AGG + chr3.3:29381869-29381888 None:intergenic 40.0%
!!! CCTTTTTTTTGGTATGTCCC+TGG + chr3.3:29382263-29382282 None:intergenic 40.0%
GCAACTTGGAGACAAGATCA+TGG + chr3.3:29381466-29381485 None:intergenic 45.0%
TGAGCGTTTGTCTGAGCTAT+TGG - chr3.3:29382520-29382539 MS.gene018969:CDS 45.0%
TGGAAGAAGTTGCTGCAACT+TGG + chr3.3:29381480-29381499 None:intergenic 45.0%
! AGAGTCAGCTCTAACTATGG+TGG - chr3.3:29381840-29381859 MS.gene018969:intron 45.0%
! CATAGTTAGAGCTGACTCTC+CGG + chr3.3:29381839-29381858 None:intergenic 45.0%
!!! TTTTTTTTTTTTTTTTTTCT+TGG + chr3.3:29382140-29382159 None:intergenic 5.0%
CTAGGGGCTAGAGACCTTAA+AGG + chr3.3:29382040-29382059 None:intergenic 50.0%
CTAGGTGCCAGAGACCTTAA+AGG + chr3.3:29382108-29382127 None:intergenic 50.0%
CTCTAGCCCCTAGGCTAATT+GGG - chr3.3:29382047-29382066 MS.gene018969:intron 50.0%
GAGCTCCTATTGCGAATCTC+TGG + chr3.3:29381500-29381519 None:intergenic 50.0%
GCTCAGACAAACGCTCACTT+AGG + chr3.3:29382517-29382536 None:intergenic 50.0%
TCTCTAGCCCCTAGGCTAAT+TGG - chr3.3:29382046-29382065 MS.gene018969:intron 50.0%
TGGTATGTCCCTGGACCTAT+AGG + chr3.3:29382254-29382273 None:intergenic 50.0%
! CGGAGAGTCAGCTCTAACTA+TGG - chr3.3:29381837-29381856 MS.gene018969:intron 50.0%
! TCGCAATAGGAGCTCTGACA+AGG - chr3.3:29381505-29381524 MS.gene018969:CDS 50.0%
!! CTTTAAGGTCTCTAGCCCCT+AGG - chr3.3:29382038-29382057 MS.gene018969:intron 50.0%
!! CTTTAAGGTCTCTGGCACCT+AGG - chr3.3:29382106-29382125 MS.gene018969:intron 50.0%
! ACTCCGGTCCCAATTAGCCT+AGG + chr3.3:29382058-29382077 None:intergenic 55.0%
! CTCCGGTCCCAATTAGCCTA+GGG + chr3.3:29382057-29382076 None:intergenic 55.0%
! GGTGTCTGGGGTTTGAACTC+CGG + chr3.3:29382006-29382025 None:intergenic 55.0%
! TCCGGTCCCAATTAGCCTAG+GGG + chr3.3:29382056-29382075 None:intergenic 55.0%
!! TTCAGCTTCGAGGGTGTTGC+AGG - chr3.3:29382448-29382467 MS.gene018969:intron 55.0%
CACGGCAAACGAGTAGCTCG+AGG - chr3.3:29381420-29381439 MS.gene018969:CDS 60.0%
CTAGCAGGAGGTCACGGTCA+CGG - chr3.3:29381402-29381421 MS.gene018969:CDS 60.0%
GCCCCTAGGCTAATTGGGAC+CGG - chr3.3:29382052-29382071 MS.gene018969:intron 60.0%
! GGTGTCTGGGGTTCGAACTC+CGG + chr3.3:29382074-29382093 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 29381398 29382595 29381398 ID=MS.gene018969
chr3.3 mRNA 29381398 29382595 29381398 ID=MS.gene018969.t1;Parent=MS.gene018969
chr3.3 exon 29382467 29382595 29382467 ID=MS.gene018969.t1.exon1;Parent=MS.gene018969.t1
chr3.3 CDS 29382467 29382595 29382467 ID=cds.MS.gene018969.t1;Parent=MS.gene018969.t1
chr3.3 exon 29381398 29381547 29381398 ID=MS.gene018969.t1.exon2;Parent=MS.gene018969.t1
chr3.3 CDS 29381398 29381547 29381398 ID=cds.MS.gene018969.t1;Parent=MS.gene018969.t1
Gene Sequence

>MS.gene018969

ATGTCTAGCAGGAGGTCACGGTCACGGCAAACGAGTAGCTCGAGGAATATCACCGACGATCAGATCCATGATCTTGTCTCCAAGTTGCAGCAACTTCTTCCAGAGATTCGCAATAGGAGCTCTGACAAGGTTTGCTCCTACATATTATTTGTTTCCTAGTCATAATCAAAAGACTAGAGTATTTATTTTTGCTTCGTTTTTTGCTTAATTACATTCATATTATTCAATTAATGTGATTTTGTTGCTTAAATACACTACCATTATTTTTTATAAAAGTCATTGGTAAGAGATAAGTAGAAAAAAGTAAATGAAAACTATAATGATGATGAGAAGAATCTAAGCTCGTAACTACCATATACTATATTTTTAATACATAGAAGAGATTAGTTTTATAGCGGATCAAAGAATCTAAGCTTGTAGAGATACCCTATTAATCTACCGGAGAGTCAGCTCTAACTATGGTGGACTCCTAAAAGCTCACAAAACAGCTCTTAATATAATTTTGCTTATAAAAAAACAAAATTTAATTGAATAAAAAAAACCGTAAAGAAATCCTTCTGAGCTTAGTTCATTTGGTAAGGGATAATGCATAATATATGCAGGGACCGGAGTTCAAACCCCAGACACCATACTTATTCACCTTTAAGGTCTCTAGCCCCTAGGCTAATTGGGACCGGAGTTCGAACCCCAGACACCATACTTATTCACCTTTAAGGTCTCTGGCACCTAGGATAATTGACCAAGAAAAAAAAAAAAAAAAAACTTGAAAGGTGCAAGAGTGATTTTGTCATTTTTAAGCATCATAAATAAATACACTAGAGTAAGTATAAGAGGGTATTTAAACCAACTTAATCCTATAGGTCCAGGGACATACCAAAAAAAAGGAACAACAATATAGGCCTAACAAATACGAGGGGATTAAGTACTTCTATCTAGCACCAGTTTTTTCCCATCTACAAGAATTGTTGATGTTTTCAATTTTTAACTATATATTTTAAGAGAATAGTTAAATATATAGCATTTACTAAATTGAATTTTACTATATCAGGTTTCAGCTTCGAGGGTGTTGCAGGAGACTTGCAACTATATTAGAAACTTGAACAGAGAAGTTGACGACCTAAGTGAGCGTTTGTCTGAGCTATTGGCTACGACAGACACAGCACAAGCAGCAATAATTAGAAATTTACTTATGCAATAG
Protein sequence

>MS.gene018969.t1

MSSRRSRSRQTSSSRNITDDQIHDLVSKLQQLLPEIRNRSSDKVSASRVLQETCNYIRNLNREVDDLSERLSELLATTDTAQAAIIRNLLMQ