AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99334

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99334.t1 MTR_1g048720 90.845 142 13 0 1 142 1 142 3.97e-93 268
MS.gene99334.t1 MTR_1g048720 90.845 142 13 0 1 142 1 142 6.54e-93 269
MS.gene99334.t1 MTR_1g048720 90.141 142 13 1 1 142 1 141 1.26e-90 262
MS.gene99334.t1 MTR_1g048720 90.141 142 13 1 1 142 1 141 2.12e-90 263
MS.gene99334.t1 MTR_1g048750 85.816 141 12 1 1 141 1 133 1.10e-82 244
MS.gene99334.t1 MTR_1g048710 83.803 142 14 2 1 142 1 133 2.19e-79 234
MS.gene99334.t1 MTR_7g090410 51.656 151 56 5 1 142 1 143 1.12e-26 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99334.t1 AT3G56970 49.669 151 55 5 1 137 1 144 5.96e-36 124
MS.gene99334.t1 AT3G56980 47.482 139 47 5 1 120 1 132 1.77e-27 102
MS.gene99334.t1 AT5G04150 59.524 84 31 1 60 140 78 161 1.49e-26 100
MS.gene99334.t1 AT2G41240 46.032 126 53 3 1 120 1 117 2.15e-26 99.8
MS.gene99334.t1 AT5G04150 59.524 84 31 1 60 140 78 161 2.80e-26 99.8
MS.gene99334.t1 AT2G41240 45.238 126 53 4 1 120 1 116 6.57e-24 93.2

Find 29 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCACCTGTTTCTGTAATTC+TGG 0.155913 1.2:+32498127 None:intergenic
TGATGCTGGTTATGGGTTAT+TGG 0.230970 1.2:+32498504 None:intergenic
ATGAACTCTGATGCTGGTTA+TGG 0.359283 1.2:+32498496 None:intergenic
AGGACTCTTGAAATTGTTGC+TGG 0.367920 1.2:+32498160 None:intergenic
CTTAGATAACCTCTTCTACT+TGG 0.368095 1.2:+32498059 None:intergenic
GATCGCGTTCACTAGCATTA+TGG 0.375108 1.2:+32498355 None:intergenic
AGTACCATTTGATCTGAAAC+AGG 0.414053 1.2:+32498285 None:intergenic
CATACCAGAATTACAGAAAC+AGG 0.417584 1.2:-32498131 MS.gene99334:CDS
TTAGATAACCTCTTCTACTT+GGG 0.422139 1.2:+32498060 None:intergenic
TCTTCCTGTTTCAGATCAAA+TGG 0.439923 1.2:-32498289 MS.gene99334:intron
ATGGGTTATTGGCTCCTCAA+AGG 0.463079 1.2:+32498515 None:intergenic
AACAATTGGATGGCCCTTTG+AGG 0.464251 1.2:-32498529 MS.gene99334:CDS
TGAACTCTGATGCTGGTTAT+GGG 0.477659 1.2:+32498497 None:intergenic
TGGGTTATTGGCTCCTCAAA+GGG 0.488564 1.2:+32498516 None:intergenic
CATGCCAAGGTCACTGCTTG+TGG 0.499479 1.2:+32498392 None:intergenic
ACAAATTATTGATCTTCTTG+CGG 0.529574 1.2:+32498331 None:intergenic
ACTTTCTCCCCAAGTAGAAG+AGG 0.556979 1.2:-32498068 MS.gene99334:CDS
CATCCAATTGTTGAAAACAT+AGG 0.558093 1.2:+32498540 None:intergenic
TGTAGAATGAACTCTGATGC+TGG 0.560692 1.2:+32498490 None:intergenic
CAATCCACAAGCAGTGACCT+TGG 0.569748 1.2:-32498396 MS.gene99334:CDS
CCAATTGTTGAAAACATAGG+AGG 0.582074 1.2:+32498543 None:intergenic
TAGATAACCTCTTCTACTTG+GGG 0.586846 1.2:+32498061 None:intergenic
ACTAGTTAAGAGAAAAGAAG+AGG 0.589176 1.2:-32498101 MS.gene99334:CDS
GTCACTGCTTGTGGATTGTG+AGG 0.591686 1.2:+32498401 None:intergenic
CACAAGCAGTGACCTTGGCA+TGG 0.602895 1.2:-32498391 MS.gene99334:CDS
CAAGCTTCTTAACCATGCCA+AGG 0.655760 1.2:+32498379 None:intergenic
ACCAGAATTACAGAAACAGG+TGG 0.656125 1.2:-32498128 MS.gene99334:CDS
GAATTACAGAAACAGGTGGA+AGG 0.659206 1.2:-32498124 MS.gene99334:CDS
TCACTGCTTGTGGATTGTGA+GGG 0.698792 1.2:+32498402 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAACAAAATCATATAGA+AGG + chr1.2:32498368-32498387 None:intergenic 15.0%
!! ATTAACAAAATCATATAGAA+GGG + chr1.2:32498367-32498386 None:intergenic 15.0%
! ACAAATTATTGATCTTCTTG+CGG + chr1.2:32498290-32498309 None:intergenic 25.0%
!! GTAATTCTGGTATGTATTTT+AGG + chr1.2:32498481-32498500 None:intergenic 25.0%
!!! TAATTTTCTTGATCAAGTTG+AGG - chr1.2:32498173-32498192 MS.gene99334:CDS 25.0%
ACTAGTTAAGAGAAAAGAAG+AGG - chr1.2:32498517-32498536 MS.gene99334:CDS 30.0%
CATCCAATTGTTGAAAACAT+AGG + chr1.2:32498081-32498100 None:intergenic 30.0%
TTAGATAACCTCTTCTACTT+GGG + chr1.2:32498561-32498580 None:intergenic 30.0%
! CTATGTTTTCAACAATTGGA+TGG - chr1.2:32498079-32498098 MS.gene99334:CDS 30.0%
CATACCAGAATTACAGAAAC+AGG - chr1.2:32498487-32498506 MS.gene99334:CDS 35.0%
CCAATTGTTGAAAACATAGG+AGG + chr1.2:32498078-32498097 None:intergenic 35.0%
TAGATAACCTCTTCTACTTG+GGG + chr1.2:32498560-32498579 None:intergenic 35.0%
TCTTCCTGTTTCAGATCAAA+TGG - chr1.2:32498329-32498348 MS.gene99334:CDS 35.0%
! AGTACCATTTGATCTGAAAC+AGG + chr1.2:32498336-32498355 None:intergenic 35.0%
! CCTCCTATGTTTTCAACAAT+TGG - chr1.2:32498075-32498094 MS.gene99334:CDS 35.0%
ACCAGAATTACAGAAACAGG+TGG - chr1.2:32498490-32498509 MS.gene99334:CDS 40.0%
AGGACTCTTGAAATTGTTGC+TGG + chr1.2:32498461-32498480 None:intergenic 40.0%
GAATTACAGAAACAGGTGGA+AGG - chr1.2:32498494-32498513 MS.gene99334:CDS 40.0%
TGTAGAATGAACTCTGATGC+TGG + chr1.2:32498131-32498150 None:intergenic 40.0%
! ATGAACTCTGATGCTGGTTA+TGG + chr1.2:32498125-32498144 None:intergenic 40.0%
! TGAACTCTGATGCTGGTTAT+GGG + chr1.2:32498124-32498143 None:intergenic 40.0%
! TGATGCTGGTTATGGGTTAT+TGG + chr1.2:32498117-32498136 None:intergenic 40.0%
!! TCCACCTGTTTCTGTAATTC+TGG + chr1.2:32498494-32498513 None:intergenic 40.0%
AACAATTGGATGGCCCTTTG+AGG - chr1.2:32498089-32498108 MS.gene99334:CDS 45.0%
ACTTTCTCCCCAAGTAGAAG+AGG - chr1.2:32498550-32498569 MS.gene99334:CDS 45.0%
CAAGCTTCTTAACCATGCCA+AGG + chr1.2:32498242-32498261 None:intergenic 45.0%
GATCGCGTTCACTAGCATTA+TGG + chr1.2:32498266-32498285 None:intergenic 45.0%
! TCACTGCTTGTGGATTGTGA+GGG + chr1.2:32498219-32498238 None:intergenic 45.0%
!! ATGGGTTATTGGCTCCTCAA+AGG + chr1.2:32498106-32498125 None:intergenic 45.0%
!! TGGGTTATTGGCTCCTCAAA+GGG + chr1.2:32498105-32498124 None:intergenic 45.0%
CAATCCACAAGCAGTGACCT+TGG - chr1.2:32498222-32498241 MS.gene99334:intron 50.0%
! GTCACTGCTTGTGGATTGTG+AGG + chr1.2:32498220-32498239 None:intergenic 50.0%
CACAAGCAGTGACCTTGGCA+TGG - chr1.2:32498227-32498246 MS.gene99334:intron 55.0%
CATGCCAAGGTCACTGCTTG+TGG + chr1.2:32498229-32498248 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 32498060 32498580 32498060 ID=MS.gene99334
chr1.2 mRNA 32498060 32498580 32498060 ID=MS.gene99334.t1;Parent=MS.gene99334
chr1.2 exon 32498290 32498580 32498290 ID=MS.gene99334.t1.exon1;Parent=MS.gene99334.t1
chr1.2 CDS 32498290 32498580 32498290 ID=cds.MS.gene99334.t1;Parent=MS.gene99334.t1
chr1.2 exon 32498060 32498197 32498060 ID=MS.gene99334.t1.exon2;Parent=MS.gene99334.t1
chr1.2 CDS 32498060 32498197 32498060 ID=cds.MS.gene99334.t1;Parent=MS.gene99334.t1
Gene Sequence

>MS.gene99334

ATGTTAGCGATATCTCCTCCTATGTTTTCAACAATTGGATGGCCCTTTGAGGAGCCAATAACCCATAACCAGCATCAGAGTTCATTCTACAAAGACACTGCTGATCAATTATTTAATTTTCTTGATCAAGTTGAGGCAGAAATTAATTCAAAAGATCCCTCACAATCCACAAGCAGTGACCTTGGCATGGTTAAGAAGCTTGTCCATAATGCTAGTGAACGCGATCGCCGCAAGAAGATCAATAATTTGTATTCATCACTTCGTTCACTTCTTCCTGTTTCAGATCAAATGGTACTTAATTAAACCCTTCTATATGATTTTGTTAATTTGTATCTCTTTTTAATACTATTGTCTTAGTATTAATTTATACATATATGTTGCAGAAGAAATTGAGCATTCCAGCAACAATTTCAAGAGTCCTAAAATACATACCAGAATTACAGAAACAGGTGGAAGGACTAGTTAAGAGAAAAGAAGAGGTCTTATTGAGACTTTCTCCCCAAGTAGAAGAGGTTATCTAA
Protein sequence

>MS.gene99334.t1

MLAISPPMFSTIGWPFEEPITHNQHQSSFYKDTADQLFNFLDQVEAEINSKDPSQSTSSDLGMVKKLVHNASERDRRKKINNLYSSLRSLLPVSDQMKKLSIPATISRVLKYIPELQKQVEGLVKRKEEVLLRLSPQVEEVI